Variant report

Variant	rs328012
Chromosome Location	chr9:108037717-108037718
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:107622708..107625182-chr9:108036132..108039068,2	K562	blood:
2	chr9:108006932..108009449-chr9:108036462..108038843,2	MCF-7	breast:
3	chr9:108031908..108034745-chr9:108037571..108039465,2	MCF-7	breast:
4	chr15:72764720..72766890-chr9:108036384..108038851,2	MCF-7	breast:
5	chr9:108029737..108031595-chr9:108037318..108040481,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261423	Chromatin interaction
ENSG00000166233	Chromatin interaction

Extended variants
information (count: 157 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:148)

rs_ID	r²[population]
rs10820792	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10820793	0.88[ASN][1000 genomes]
rs10820795	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs10820796	0.82[ASN][1000 genomes]
rs10991598	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10991600	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10991601	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs10991607	0.88[ASN][1000 genomes]
rs10991611	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs10991612	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs10991613	0.88[ASN][1000 genomes]
rs10991614	0.88[ASN][1000 genomes]
rs10991617	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs10991618	1.00[CHB][hapmap]
rs12335779	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs12336008	0.88[ASN][1000 genomes]
rs12343678	0.85[ASN][1000 genomes]
rs12347364	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs12348136	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs12686574	0.88[ASN][1000 genomes]
rs167867	0.85[ASN][1000 genomes]
rs1705490	0.85[ASN][1000 genomes]
rs1705491	0.85[ASN][1000 genomes]
rs170582	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs179177	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs182756	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[ASN][1000 genomes]
rs186617	0.88[ASN][1000 genomes]
rs189020	0.88[ASN][1000 genomes]
rs193007	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs193008	0.90[CHB][hapmap];0.88[ASN][1000 genomes]
rs193009	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2004725	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2089807	0.88[ASN][1000 genomes]
rs2100044	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs227887	0.84[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs227888	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2441214	0.85[ASN][1000 genomes]
rs2900397	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs327944	0.88[ASN][1000 genomes]
rs327945	0.87[ASN][1000 genomes]
rs327946	0.88[ASN][1000 genomes]
rs327947	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs327948	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs327949	0.88[ASN][1000 genomes]
rs327950	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs327954	0.85[ASN][1000 genomes]
rs327955	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs327956	1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[ASN][1000 genomes]
rs327958	1.00[CHB][hapmap]
rs327959	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs327960	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs327961	0.85[ASN][1000 genomes]
rs327962	0.85[ASN][1000 genomes]
rs327963	0.85[ASN][1000 genomes]
rs327964	0.85[ASN][1000 genomes]
rs327966	0.85[ASN][1000 genomes]
rs327967	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs327968	0.85[ASN][1000 genomes]
rs327975	0.88[ASN][1000 genomes]
rs327976	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs327977	0.88[ASN][1000 genomes]
rs327978	0.88[ASN][1000 genomes]
rs327979	0.88[ASN][1000 genomes]
rs327980	0.88[ASN][1000 genomes]
rs327981	0.88[ASN][1000 genomes]
rs327982	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs327983	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs327984	1.00[CHB][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs327985	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs327986	0.88[ASN][1000 genomes]
rs327987	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs327990	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs327991	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs327992	1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[ASN][1000 genomes]
rs327993	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs327995	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs327996	0.85[ASN][1000 genomes]
rs327997	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs327998	0.84[ASN][1000 genomes]
rs327999	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs328000	0.85[ASN][1000 genomes]
rs328001	0.88[ASN][1000 genomes]
rs328002	0.88[ASN][1000 genomes]
rs328003	0.88[ASN][1000 genomes]
rs328004	0.88[ASN][1000 genomes]
rs328005	0.88[ASN][1000 genomes]
rs328006	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs328007	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs328008	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs328010	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs328011	0.88[ASN][1000 genomes]
rs328013	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs328014	0.84[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs328015	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs328017	0.88[ASN][1000 genomes]
rs328018	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs328019	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs328020	0.85[ASN][1000 genomes]
rs328021	0.85[ASN][1000 genomes]
rs328022	1.00[CHB][hapmap]
rs35144319	0.85[ASN][1000 genomes]
rs35584395	0.88[ASN][1000 genomes]
rs365629	0.90[CHB][hapmap]
rs366144	0.85[ASN][1000 genomes]
rs370629	0.85[ASN][1000 genomes]
rs374445	0.85[ASN][1000 genomes]
rs375034	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs376926	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs377129	0.85[ASN][1000 genomes]
rs378467	1.00[CHB][hapmap]
rs380104	1.00[CHB][hapmap]
rs380667	0.85[ASN][1000 genomes]
rs382940	0.88[ASN][1000 genomes]
rs383126	0.90[CHB][hapmap];0.85[CHD][hapmap]
rs383272	1.00[CHB][hapmap]
rs384924	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs384947	1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[ASN][1000 genomes]
rs386565	1.00[CHB][hapmap]
rs388679	0.85[ASN][1000 genomes]
rs390336	0.85[ASN][1000 genomes]
rs390701	0.85[ASN][1000 genomes]
rs391943	0.85[ASN][1000 genomes]
rs398454	0.85[ASN][1000 genomes]
rs403316	0.85[ASN][1000 genomes]
rs410897	0.85[ASN][1000 genomes]
rs416641	1.00[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs418057	0.88[ASN][1000 genomes]
rs419443	0.85[ASN][1000 genomes]
rs420717	1.00[CHB][hapmap]
rs422084	1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[ASN][1000 genomes]
rs423976	0.85[ASN][1000 genomes]
rs424495	1.00[CHB][hapmap];0.95[CHD][hapmap]
rs435379	0.85[ASN][1000 genomes]
rs438299	0.85[ASN][1000 genomes]
rs439308	0.85[ASN][1000 genomes]
rs440290	0.88[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.86[MKK][hapmap]
rs442605	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs443094	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs445964	0.85[ASN][1000 genomes]
rs446641	0.82[ASN][1000 genomes]
rs448836	0.82[ASN][1000 genomes]
rs6479305	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs7020772	0.81[ASN][1000 genomes]
rs7020982	0.90[CHB][hapmap];0.95[CHD][hapmap];0.88[ASN][1000 genomes]
rs7021008	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs7039398	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs7858967	0.82[ASN][1000 genomes]
rs7866947	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv831678	chr9:107923522-108112813	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv893685	chr9:107940737-108083485	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv893686	chr9:107968330-108083485	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv893687	chr9:107973277-108083485	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv893688	chr9:107974761-108083485	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv893689	chr9:107978563-108130606	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv893690	chr9:107992706-108083485	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs328012	ZNF189	cis	cerebellum	SCAN
rs328012	SLC44A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108017200-108040800	Weak transcription	HMEC	breast
2	chr9:108020800-108040000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr9:108021400-108039200	Weak transcription	Pancreas	Pancrea
4	chr9:108021400-108042600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr9:108021600-108043200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:108022400-108053600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr9:108022800-108041000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr9:108022800-108042400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr9:108022800-108046000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr9:108023000-108043200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr9:108023600-108045200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr9:108025200-108042400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr9:108027000-108039800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:108027200-108051000	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr9:108028400-108053000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr9:108030000-108045200	Enhancers	Brain Hippocampus Middle	brain
17	chr9:108031200-108045200	Weak transcription	Liver	Liver
18	chr9:108032000-108040400	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr9:108032200-108044200	Weak transcription	Small Intestine	intestine
20	chr9:108032400-108040800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr9:108032400-108043800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:108032800-108040800	Weak transcription	Psoas Muscle	Psoas
23	chr9:108033200-108038000	Weak transcription	Fetal Thymus	thymus
24	chr9:108033200-108056200	Weak transcription	Primary T cells from cord blood	blood
25	chr9:108033400-108042000	Weak transcription	Rectal Smooth Muscle	rectum
26	chr9:108033400-108048400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr9:108033600-108039000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:108033800-108038800	Weak transcription	Fetal Brain Female	brain
29	chr9:108033800-108044800	Weak transcription	HepG2	liver
30	chr9:108033800-108049400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr9:108033800-108052800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr9:108034000-108049800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:108034200-108053600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:108034400-108041400	Enhancers	Brain Substantia Nigra	brain
35	chr9:108035000-108038800	Weak transcription	Fetal Intestine Small	intestine
36	chr9:108035000-108043200	Weak transcription	Stomach Mucosa	stomach
37	chr9:108035600-108038200	Enhancers	Brain Angular Gyrus	brain
38	chr9:108035800-108041400	Enhancers	Brain Anterior Caudate	brain
39	chr9:108036000-108039800	Enhancers	Fetal Brain Male	brain
40	chr9:108036000-108044000	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr9:108036200-108038000	Enhancers	Brain Cingulate Gyrus	brain
42	chr9:108037000-108039600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr9:108037400-108037800	Enhancers	Duodenum Mucosa	Duodenum
44	chr9:108037400-108039000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr9:108037600-108037800	Enhancers	Fetal Intestine Large	intestine
46	chr9:108037600-108037800	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr9:108037600-108038000	Enhancers	iPS-18 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links