Variant report

Variant	rs9812200
Chromosome Location	chr3:48695667-48695668
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:48616186..48618444-chr3:48693740..48696673,2	MCF-7	breast:
2	chr3:48671879..48673850-chr3:48694137..48695935,2	MCF-7	breast:
3	chr3:48682961..48685623-chr3:48693830..48696752,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000225697	Chromatin interaction
ENSG00000211535	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1003649	0.83[GIH][hapmap]
rs10470687	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs11557629	0.83[EUR][1000 genomes]
rs11706983	1.00[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs11708786	1.00[GIH][hapmap]
rs11713694	0.83[GIH][hapmap]
rs11719291	1.00[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs12107252	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12107418	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12497850	0.87[LWK][hapmap];0.90[YRI][hapmap]
rs12715429	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13060933	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13063312	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13070798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13074318	0.83[GIH][hapmap]
rs13076269	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13090013	0.83[EUR][1000 genomes]
rs13091944	1.00[JPT][hapmap]
rs13096357	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13319651	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13324119	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13324142	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13434258	1.00[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs17080289	0.80[CHD][hapmap];1.00[GIH][hapmap]
rs17080319	0.83[EUR][1000 genomes]
rs2006871	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs2276850	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2276852	0.89[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2286651	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2286652	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2302295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2310996	0.94[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2310997	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28452701	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2854394	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs28567949	0.83[EUR][1000 genomes]
rs28657585	0.81[EUR][1000 genomes]
rs34037363	0.83[GIH][hapmap]
rs34096717	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34153629	0.83[EUR][1000 genomes]
rs34368826	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34577723	0.81[EUR][1000 genomes]
rs34638686	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35064573	1.00[GIH][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs3733086	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3821875	0.81[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821876	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3969942	0.83[GIH][hapmap]
rs4858798	0.90[YRI][hapmap]
rs4858828	0.90[YRI][hapmap]
rs4858831	0.90[YRI][hapmap]
rs57334642	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6768448	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6773261	0.90[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6781283	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6788650	0.90[YRI][hapmap]
rs6792156	0.82[ASW][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6792525	0.84[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs68042649	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6806059	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs73078349	0.80[EUR][1000 genomes]
rs73078362	0.80[EUR][1000 genomes]
rs740787	1.00[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.96[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7428949	1.00[JPT][hapmap]
rs7620853	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7631574	0.94[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9809222	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9810549	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9810991	0.83[GIH][hapmap]
rs9811027	0.83[EUR][1000 genomes]
rs9811318	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9812977	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9821797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9830581	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9836462	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9837687	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9841602	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9843316	0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9850102	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9851771	0.83[GIH][hapmap]
rs9868809	0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.83[EUR][1000 genomes]
rs9869698	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9871180	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9873726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9875911	0.83[GIH][hapmap]
rs9878063	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9878950	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9881877	1.00[GIH][hapmap]
rs9882549	1.00[GIH][hapmap]
rs9882962	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers 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	52 gene(s)	inside rSNPs	diseases
3	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv818138	chr3:48610925-48731487	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv590246	chr3:48628014-48721040	Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv590247	chr3:48661985-48801929	Transcr. at gene 5' and 3' Strong transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
8	nsv876763	chr3:48669648-48710310	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs9812200	WDR6	cis	Adipose Subcutaneous	GTEx
rs9812200	WDR6	cis	Esophagus Mucosa	GTEx
rs9812200	WDR6	cis	multi-tissue	Pritchard
rs9812200	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9812200	WDR6	cis	Artery Tibial	GTEx
rs9812200	WDR6	cis	lung	GTEx
rs9812200	USP4	cis	multi-tissue	Pritchard
rs9812200	WDR6	cis	lymphoblastoid	seeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48675000-48697200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:48693400-48696800	Enhancers	Fetal Brain Male	brain
3	chr3:48694000-48698800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:48694200-48695800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:48694200-48696200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:48694200-48696400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:48694200-48696400	Weak transcription	HepG2	liver
8	chr3:48694200-48696800	Weak transcription	A549	lung
9	chr3:48694200-48698400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:48694200-48698600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr3:48694200-48698600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:48694200-48698600	Weak transcription	HSMMtube	muscle
13	chr3:48694200-48699000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr3:48694400-48695800	Weak transcription	Brain Anterior Caudate	brain
15	chr3:48694400-48695800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:48694400-48696200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr3:48694400-48696400	Weak transcription	Brain Angular Gyrus	brain
18	chr3:48694400-48696800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:48694400-48697400	Weak transcription	Brain Hippocampus Middle	brain
20	chr3:48694400-48698200	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:48694400-48698600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:48694400-48698600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:48694400-48698800	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr3:48694400-48698800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:48694400-48698800	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:48694400-48698800	Weak transcription	HUVEC	blood vessel
27	chr3:48694600-48696400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:48694600-48698800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:48694600-48698800	Weak transcription	Brain Substantia Nigra	brain
30	chr3:48694800-48696600	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr3:48694800-48696800	Weak transcription	Lung	lung
32	chr3:48694800-48697400	Weak transcription	Esophagus	oesophagus
33	chr3:48694800-48697600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr3:48694800-48698600	Weak transcription	Left Ventricle	heart
35	chr3:48694800-48698800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr3:48694800-48698800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr3:48694800-48698800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:48695000-48696200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:48695000-48696200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:48695000-48696400	Transcr. at gene 5' and 3'	Fetal Brain Female	brain
41	chr3:48695000-48696800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr3:48695000-48696800	Weak transcription	Spleen	Spleen
43	chr3:48695000-48698200	Weak transcription	Pancreas	Pancrea
44	chr3:48695000-48698200	Weak transcription	Right Ventricle	heart
45	chr3:48695000-48698800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr3:48695200-48696200	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr3:48695400-48698600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr3:48695600-48696200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:48695600-48698000	Genic enhancers	Brain Germinal Matrix	brain
50	chr3:48695600-48698200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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