Variant report

Variant	rs12336472
Chromosome Location	chr9:140527433-140527434
allele	G/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:140498669..140500543-chr9:140525332..140527942,2	K562	blood:
2	chr9:140523195..140524833-chr9:140524940..140527470,2	MCF-7	breast:
3	chr9:140470766..140472473-chr9:140525888..140528699,2	MCF-7	breast:
4	chr9:140499757..140501674-chr9:140525440..140528295,2	MCF-7	breast:
5	chr9:140519645..140523590-chr9:140526467..140528234,3	K562	blood:
6	chr9:140509926..140512200-chr9:140526442..140528104,2	MCF-7	breast:
7	chr9:140520368..140523590-chr9:140524404..140528000,5	K562	blood:
8	chr9:140515440..140517099-chr9:140525922..140527990,2	K562	blood:
9	chr9:140512386..140514034-chr9:140526811..140529499,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000203993	Chromatin interaction
ENSG00000197070	Chromatin interaction
ENSG00000181090	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10117888	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11137126	1.00[AMR][1000 genomes]
rs11137164	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12335931	1.00[AMR][1000 genomes]
rs12336683	1.00[GIH][hapmap]
rs12341344	1.00[AMR][1000 genomes]
rs12341948	1.00[GIH][hapmap]
rs12342671	1.00[AMR][1000 genomes]
rs12344692	1.00[ASW][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes]
rs12346297	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12352124	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17065610	1.00[GIH][hapmap]
rs17065647	1.00[GIH][hapmap]
rs2259872	1.00[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:30 , 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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12336472	AHSP	trans	lymphoblastoid	seeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:140515600-140535400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr9:140515600-140539800	Weak transcription	HMEC	breast
3	chr9:140516000-140532200	Weak transcription	NHEK	skin
4	chr9:140516000-140533200	Weak transcription	Esophagus	oesophagus
5	chr9:140516200-140558800	Weak transcription	NH-A	brain
6	chr9:140516400-140535200	Weak transcription	Fetal Intestine Large	intestine
7	chr9:140519200-140527800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr9:140519200-140536600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:140520000-140535400	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr9:140520000-140540400	Weak transcription	Brain Germinal Matrix	brain
11	chr9:140520000-140549800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr9:140521200-140529800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr9:140522000-140527600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr9:140522000-140527600	Enhancers	Primary B cells from peripheral blood	blood
15	chr9:140522400-140527600	Enhancers	Liver	Liver
16	chr9:140522400-140527600	Enhancers	Colon Smooth Muscle	Colon
17	chr9:140522800-140532000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr9:140523200-140534200	Weak transcription	Colonic Mucosa	Colon
19	chr9:140523200-140534200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr9:140523200-140538200	Weak transcription	HSMMtube	muscle
21	chr9:140523400-140527600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr9:140523400-140527800	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr9:140523400-140529000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
24	chr9:140523400-140533200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr9:140523400-140533200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:140523400-140533200	Weak transcription	Dnd41	blood
27	chr9:140523400-140563400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr9:140523600-140527800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr9:140523600-140533200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr9:140523600-140535400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr9:140524200-140529000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr9:140524800-140527600	Enhancers	Primary hematopoietic stem cells	blood
33	chr9:140524800-140527800	Enhancers	Ovary	ovary
34	chr9:140525000-140527600	Enhancers	Right Ventricle	heart
35	chr9:140525000-140527800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:140525000-140533200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr9:140525200-140527600	Enhancers	Lung	lung
38	chr9:140525400-140527600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr9:140525400-140527800	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr9:140525400-140528200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr9:140525400-140533200	Weak transcription	Stomach Mucosa	stomach
42	chr9:140525400-140535400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr9:140525400-140538200	Weak transcription	A549	lung
44	chr9:140525600-140532800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr9:140525600-140533200	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr9:140525600-140533200	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr9:140525800-140534200	Weak transcription	Small Intestine	intestine
48	chr9:140526000-140527600	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr9:140526200-140527600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr9:140526200-140527600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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