Variant report

Variant	rs2501556
Chromosome Location	chr9:140577178-140577179
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:140576034..140577675-chr9:140577860..140579633,2	K562	blood:
2	chr9:140572665..140574180-chr9:140575707..140577465,2	MCF-7	breast:
3	chr9:140575772..140578110-chr9:140581931..140583477,2	MCF-7	breast:
4	chr9:140576082..140579236-chr9:140582001..140584709,3	MCF-7	breast:
5	chr9:140571660..140574434-chr9:140575012..140577308,2	MCF-7	breast:
6	chr9:140569780..140572620-chr9:140576768..140579766,2	K562	blood:

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10110	0.82[CHB][hapmap]
rs10123486	0.88[ASN][1000 genomes]
rs1045777	0.85[CHB][hapmap]
rs10481734	0.90[ASN][1000 genomes]
rs10732688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10746564	0.90[ASN][1000 genomes]
rs10780179	1.00[CHB][hapmap]
rs10780180	0.87[ASN][1000 genomes]
rs10780181	0.90[ASN][1000 genomes]
rs10780182	0.90[ASN][1000 genomes]
rs10780183	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10780184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10867049	0.88[ASN][1000 genomes]
rs10867050	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10867051	1.00[CHB][hapmap];0.94[ASN][1000 genomes]
rs10867052	0.92[ASN][1000 genomes]
rs10867053	0.92[ASN][1000 genomes]
rs10867054	0.92[ASN][1000 genomes]
rs11137135	0.82[CHB][hapmap]
rs11137140	1.00[CHB][hapmap]
rs11137141	1.00[CHB][hapmap]
rs11137158	1.00[CHB][hapmap]
rs11137163	1.00[CHB][hapmap]
rs11137167	1.00[CHB][hapmap]
rs11137169	1.00[CHB][hapmap]
rs11137172	1.00[CHB][hapmap]
rs11137177	0.92[ASN][1000 genomes]
rs11137178	0.92[ASN][1000 genomes]
rs11137179	0.92[ASN][1000 genomes]
rs11137182	0.85[ASN][1000 genomes]
rs12551649	0.92[ASN][1000 genomes]
rs12683290	0.82[CHB][hapmap]
rs13290032	1.00[JPT][hapmap]
rs13296028	1.00[CHB][hapmap]
rs17496354	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1776776	1.00[CHB][hapmap]
rs1891628	1.00[CHB][hapmap]
rs2014103	0.92[ASN][1000 genomes]
rs2094623	1.00[CHB][hapmap]
rs2183138	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2257839	1.00[CHB][hapmap]
rs2297004	1.00[CHB][hapmap]
rs2501559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2501560	0.92[ASN][1000 genomes]
rs2501567	1.00[CHB][hapmap]
rs2501568	1.00[CHB][hapmap]
rs2987618	1.00[CHB][hapmap]
rs2987621	1.00[CHB][hapmap]
rs36088123	0.92[ASN][1000 genomes]
rs3849856	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3860888	0.83[ASN][1000 genomes]
rs3895387	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4246177	1.00[CHB][hapmap]
rs4567119	0.92[ASN][1000 genomes]
rs4962227	1.00[CHB][hapmap]
rs4979638	0.88[ASN][1000 genomes]
rs4979651	0.88[ASN][1000 genomes]
rs4979652	0.88[ASN][1000 genomes]
rs4979653	0.92[ASN][1000 genomes]
rs4979655	0.94[ASN][1000 genomes]
rs4979656	0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs4979657	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7024179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7043932	1.00[CHB][hapmap]
rs821313	1.00[CHB][hapmap]
rs863701	0.82[CHB][hapmap]
rs9410116	0.92[ASN][1000 genomes]
rs950078	0.82[CHB][hapmap]
rs975978	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:34 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894499	chr9:139810595-140734161	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	376 gene(s)	inside rSNPs	diseases
2	nsv531664	chr9:140110329-140725056	ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	275 gene(s)	inside rSNPs	diseases
3	nsv531654	chr9:140110329-141033187	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	281 gene(s)	inside rSNPs	diseases
4	nsv932633	chr9:140240417-141053535	Enhancers Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
5	nsv1035524	chr9:140251014-140751633	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
6	nsv1053628	chr9:140260666-141005637	Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
7	nsv534215	chr9:140286134-141008915	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	105 gene(s)	inside rSNPs	n/a
8	nsv1035388	chr9:140306746-140654768	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	96 gene(s)	inside rSNPs	n/a
9	nsv1039672	chr9:140343466-140707505	Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	n/a
10	nsv540358	chr9:140343466-140707505	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	85 gene(s)	inside rSNPs	n/a
11	nsv1041512	chr9:140350404-140612859	Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	n/a
12	nsv540359	chr9:140350404-140612859	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	n/a
13	nsv616023	chr9:140372570-140602887	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	n/a
14	nsv531603	chr9:140378700-140590977	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	n/a
15	nsv531665	chr9:140378700-141073897	Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	n/a
16	nsv868924	chr9:140407572-141053525	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	n/a
17	nsv1039933	chr9:140408112-141005637	Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	n/a
18	nsv531666	chr9:140409395-141015925	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	n/a
19	nsv831763	chr9:140439831-140614021	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	n/a
20	esv3398333	chr9:140451462-140814795	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	n/a
21	nsv1052036	chr9:140452641-141018985	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
22	nsv540365	chr9:140452641-141018985	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
23	nsv949702	chr9:140466816-141027939	Strong transcription Active TSS Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	n/a
24	nsv531667	chr9:140468821-140936261	Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	n/a
25	nsv531668	chr9:140492807-140986221	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	n/a
26	nsv531669	chr9:140514663-140852911	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	n/a
27	nsv1053192	chr9:140532404-141005637	Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
28	nsv540366	chr9:140532404-141005637	Weak transcription Strong transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	n/a
29	nsv532478	chr9:140535164-140786943	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	n/a
30	nsv894676	chr9:140536098-140734161	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	n/a
31	nsv534573	chr9:140550908-140757122	Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	n/a
32	esv3332301	chr9:140570414-140663373	Genic enhancers Enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
33	nsv1038506	chr9:140575692-140622394	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
34	nsv1038090	chr9:140575692-141005637	Genic enhancers ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	15 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2501556	PNPLA7	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:140564000-140591200	Weak transcription	Aorta	Aorta
2	chr9:140564200-140599400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr9:140565600-140577200	Weak transcription	HSMM	muscle
4	chr9:140567800-140582800	Weak transcription	A549	lung
5	chr9:140568000-140579600	Weak transcription	Osteobl	bone
6	chr9:140568200-140579600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr9:140568200-140579800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr9:140568200-140586000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:140568600-140577400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr9:140568600-140585200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr9:140568800-140579800	Weak transcription	NHLF	lung
12	chr9:140568800-140583200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr9:140568800-140583200	Weak transcription	HepG2	liver
14	chr9:140569200-140582600	Weak transcription	Hela-S3	cervix
15	chr9:140569200-140583200	Weak transcription	Adipose Nuclei	Adipose
16	chr9:140569200-140583200	Weak transcription	Liver	Liver
17	chr9:140569400-140577200	Weak transcription	Brain Hippocampus Middle	brain
18	chr9:140569400-140577200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:140569400-140577200	Weak transcription	Brain Substantia Nigra	brain
20	chr9:140569400-140582800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr9:140569400-140582800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr9:140569400-140583200	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr9:140569600-140589600	Weak transcription	Stomach Smooth Muscle	stomach
24	chr9:140569600-140594600	Weak transcription	NHEK	skin
25	chr9:140571000-140577600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:140571800-140586000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr9:140572600-140578600	Enhancers	HUES64 Cell Line	embryonic stem cell
28	chr9:140572800-140577600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr9:140572800-140578000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr9:140573000-140578000	Enhancers	Primary B cells from peripheral blood	blood
31	chr9:140573000-140638400	Weak transcription	Small Intestine	intestine
32	chr9:140573200-140578000	Enhancers	Skeletal Muscle Male	skeletal muscle
33	chr9:140573400-140579000	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr9:140573400-140580000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr9:140573600-140578600	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr9:140573800-140577800	Enhancers	HUES6 Cell Line	embryonic stem cell
37	chr9:140573800-140578200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr9:140574000-140577600	Enhancers	HUES48 Cell Line	embryonic stem cell
39	chr9:140574000-140577800	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr9:140574000-140579000	Weak transcription	Primary neutrophils fromperipheralblood	blood
41	chr9:140574000-140579400	Enhancers	H1 Cell Line	embryonic stem cell
42	chr9:140574000-140580400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:140574000-140582800	Weak transcription	Psoas Muscle	Psoas
44	chr9:140574000-140592400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr9:140574200-140577800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr9:140574200-140580000	Weak transcription	NH-A	brain
47	chr9:140574200-140595400	Weak transcription	Dnd41	blood
48	chr9:140574400-140577200	Weak transcription	Brain Anterior Caudate	brain
49	chr9:140574400-140577200	Weak transcription	Brain Germinal Matrix	brain
50	chr9:140574400-140577400	Enhancers	Left Ventricle	heart

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