Variant report

Variant	rs2488592
Chromosome Location	chr9:140429413-140429414
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:140427835..140429829-chr9:140435567..140437956,2	MCF-7	breast:
2	chr9:140133452..140136441-chr9:140429193..140431357,3	K562	blood:
3	chr9:140428151..140432406-chr9:140438574..140446219,7	MCF-7	breast:
4	chr9:140352534..140355006-chr9:140428668..140431073,2	MCF-7	breast:
5	chr9:140428399..140433224-chr9:140435780..140438128,4	MCF-7	breast:
6	chr9:140196288..140198900-chr9:140428993..140430917,2	K562	blood:
7	chr9:140427985..140429515-chr9:140431192..140432744,2	K562	blood:
8	chr9:140428683..140431076-chr9:140437788..140439883,2	K562	blood:
9	chr9:140323536..140326071-chr9:140429160..140430978,2	K562	blood:
10	chr9:140428693..140430574-chr9:140440838..140442352,2	MCF-7	breast:
11	chr9:140429112..140429930-chr9:140506255..140506842,2	MCF-7	breast:
12	chr9:140427918..140430895-chr9:140433135..140434802,2	K562	blood:
13	chr9:140428970..140429596-chr9:140445585..140446090,2	MCF-7	breast:
14	chr9:140426992..140430139-chr9:140444541..140447373,3	MCF-7	breast:
15	chr9:140429171..140429941-chr9:140445580..140446112,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000188229	Chromatin interaction
ENSG00000263933	Chromatin interaction
ENSG00000165802	Chromatin interaction
ENSG00000182154	Chromatin interaction
ENSG00000198435	Chromatin interaction
ENSG00000130653	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10867123	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1099298	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11793453	0.83[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11795029	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1776771	0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2488593	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28875616	0.87[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs3737320	0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs3750383	0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7023481	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs72619354	0.83[AMR][1000 genomes]
rs7848838	0.95[ASN][1000 genomes]
rs821309	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[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	nsv894442	chr9:139544437-140462099	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv894452	chr9:139598108-140523429	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	450 gene(s)	inside rSNPs	diseases
3	nsv894474	chr9:139694521-140432318	Genic enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
4	nsv894487	chr9:139725120-140449582	Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	363 gene(s)	inside rSNPs	diseases
5	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
6	nsv894502	chr9:139823670-140487108	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
7	nsv894523	chr9:139860631-140462099	Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
8	nsv894564	chr9:139906359-140432318	Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	310 gene(s)	inside rSNPs	diseases
9	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
10	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
11	nsv1047563	chr9:140219047-140560852	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
12	nsv540357	chr9:140219047-140560852	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	97 gene(s)	inside rSNPs	diseases
13	nsv531602	chr9:140240417-140535223	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	96 gene(s)	inside rSNPs	diseases
14	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
15	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
16	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
17	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
18	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
19	nsv831762	chr9:140338779-140514107	Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	n/a
20	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
21	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
22	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
23	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
24	nsv616022	chr9:140372570-140523429	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	n/a
25	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
26	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
27	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
28	nsv894663	chr9:140382705-140454791	Weak transcription Strong transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	n/a
29	nsv540362	chr9:140401645-140452700	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	n/a
30	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
31	nsv540363	chr9:140408112-140447920	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	n/a
32	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
33	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
34	nsv616024	chr9:140414410-140536098	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:140376800-140444000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:140377000-140437000	Weak transcription	Left Ventricle	heart
3	chr9:140408600-140444400	Weak transcription	Esophagus	oesophagus
4	chr9:140411200-140444200	Weak transcription	Right Atrium	heart
5	chr9:140414600-140438400	Weak transcription	Colonic Mucosa	Colon
6	chr9:140419600-140430800	Weak transcription	Spleen	Spleen
7	chr9:140426400-140435800	Weak transcription	HSMMtube	muscle
8	chr9:140428600-140429800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr9:140429000-140429600	Enhancers	Pancreas	Pancrea
10	chr9:140429000-140429600	Flanking Active TSS	Hela-S3	cervix
11	chr9:140429000-140429800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr9:140429000-140429800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:140429000-140429800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr9:140429000-140429800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr9:140429000-140429800	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr9:140429000-140429800	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr9:140429000-140429800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr9:140429000-140429800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr9:140429000-140429800	Enhancers	Adipose Nuclei	Adipose
20	chr9:140429000-140429800	Enhancers	Duodenum Mucosa	Duodenum
21	chr9:140429000-140429800	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr9:140429000-140429800	Enhancers	Fetal Kidney	kidney
23	chr9:140429000-140429800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr9:140429000-140430000	Enhancers	Primary T cells fromperipheralblood	blood
25	chr9:140429000-140430000	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr9:140429000-140430000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr9:140429000-140430000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr9:140429000-140430000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:140429000-140430000	Enhancers	Liver	Liver
30	chr9:140429000-140430000	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr9:140429000-140430000	Enhancers	GM12878-XiMat	blood
32	chr9:140429000-140430200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr9:140429200-140429600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr9:140429200-140429600	Enhancers	Aorta	Aorta
35	chr9:140429200-140429600	Enhancers	Fetal Brain Male	brain
36	chr9:140429200-140429600	Enhancers	Right Ventricle	heart
37	chr9:140429200-140429600	Flanking Active TSS	Osteobl	bone
38	chr9:140429200-140429800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr9:140429200-140429800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr9:140429200-140429800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr9:140429200-140429800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:140429200-140429800	Enhancers	Primary B cells from cord blood	blood
43	chr9:140429200-140429800	Enhancers	Primary B cells from peripheral blood	blood
44	chr9:140429200-140429800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr9:140429200-140429800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
46	chr9:140429200-140429800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr9:140429200-140429800	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr9:140429200-140429800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr9:140429200-140429800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr9:140429200-140429800	Enhancers	Muscle Satellite Cultured Cells	--

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