Variant report

Variant	rs11130214
Chromosome Location	chr3:49735746-49735747
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49735716-49736116	K562	blood:	n/a	n/a
2	POLR2A	chr3:49732776-49736804	K562	blood:	n/a	n/a
3	POLR2A	chr3:49735736-49735829	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49727338..49730126-chr3:49733777..49735933,2	K562	blood:
2	chr3:49735446..49741255-chr3:49749875..49755830,7	K562	blood:
3	chr3:49735420..49737608-chr3:49739915..49742749,3	K562	blood:
4	chr3:49734358..49736524-chr3:49759903..49761802,2	K562	blood:

Variant related genes	Relation type
RNF123	TF binding region
ENSG00000173540	Chromatin interaction
ENSG00000164068	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10049413	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1049256	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs10865958	0.85[ASN][1000 genomes]
rs10865959	0.88[CHB][hapmap];0.88[YRI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130218	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs11130219	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs11130221	0.87[JPT][hapmap];0.92[ASN][1000 genomes]
rs1128535	0.85[ASN][1000 genomes]
rs11709680	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs11710675	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11714957	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11715304	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11716575	0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs11717256	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11717463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11920900	1.00[CEU][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12381242	0.94[ASN][1000 genomes]
rs12490656	0.87[ASN][1000 genomes]
rs12496226	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13063621	0.92[ASN][1000 genomes]
rs13084243	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13085679	0.85[ASN][1000 genomes]
rs13086130	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13086465	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13090611	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1317140	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes]
rs13316065	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1491986	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs1799843	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1799845	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2234385	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2234391	0.96[CHD][hapmap];0.89[GIH][hapmap];0.85[ASN][1000 genomes]
rs2246832	0.82[ASN][1000 genomes]
rs2247036	0.82[ASN][1000 genomes]
rs2271960	0.96[CHD][hapmap];0.87[GIH][hapmap];0.82[ASN][1000 genomes]
rs2271961	0.96[CHD][hapmap];0.85[GIH][hapmap];0.82[ASN][1000 genomes]
rs2276864	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[ASN][1000 genomes]
rs2291542	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307021	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2352967	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2352974	0.96[CHD][hapmap];0.91[GIH][hapmap];0.82[ASN][1000 genomes]
rs2352975	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34451146	0.92[ASN][1000 genomes]
rs34522271	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34614773	0.94[ASN][1000 genomes]
rs34735338	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35210174	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35261599	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs35474403	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3749237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3749240	1.00[CHB][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs3749241	0.96[ASN][1000 genomes]
rs3811695	0.92[ASN][1000 genomes]
rs3811696	0.94[ASN][1000 genomes]
rs3819325	0.81[ASN][1000 genomes]
rs4768	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4855841	0.91[ASN][1000 genomes]
rs4855850	0.92[ASN][1000 genomes]
rs4855862	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs4855867	0.82[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs57648519	0.92[ASN][1000 genomes]
rs59906301	0.90[ASN][1000 genomes]
rs60205400	0.92[ASN][1000 genomes]
rs62260715	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62260719	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62260729	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6446295	0.94[ASN][1000 genomes]
rs6766836	0.92[ASN][1000 genomes]
rs6775384	0.92[CHD][hapmap];0.85[ASN][1000 genomes]
rs6785549	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6802890	0.91[CHD][hapmap];0.91[GIH][hapmap];0.89[ASN][1000 genomes]
rs6804655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs695238	0.96[CHD][hapmap];0.89[GIH][hapmap];0.85[ASN][1000 genomes]
rs71324996	0.83[EUR][1000 genomes]
rs7372725	0.88[ASN][1000 genomes]
rs7372730	0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs7372966	0.95[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs7374183	0.95[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs7374277	0.88[ASN][1000 genomes]
rs7429353	0.88[ASN][1000 genomes]
rs7431078	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7431106	0.82[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.92[ASN][1000 genomes]
rs7618501	0.93[ASN][1000 genomes]
rs7618519	0.94[ASN][1000 genomes]
rs7629936	0.87[ASW][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7634886	0.89[ASN][1000 genomes]
rs7634902	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs7645061	0.96[CHD][hapmap];0.89[GIH][hapmap];0.85[ASN][1000 genomes]
rs7648987	0.96[CHD][hapmap];0.89[GIH][hapmap];0.85[ASN][1000 genomes]
rs7649348	1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs9814765	0.89[ASN][1000 genomes]
rs9815766	0.82[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs9819511	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9850465	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9853458	0.94[ASN][1000 genomes]
rs9855505	0.95[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs9859153	0.82[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs9865480	0.94[ASN][1000 genomes]
rs9871654	0.91[ASN][1000 genomes]
rs9872864	0.95[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs9873183	0.94[ASN][1000 genomes]
rs9876508	1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs9882639	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv508217	chr3:49615446-49769896	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv1796352	chr3:49687101-49949959	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh 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	90 gene(s)	inside rSNPs	diseases
3	esv1825898	chr3:49688948-49764849	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	esv1808511	chr3:49689880-49744825	Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
5	nsv820990	chr3:49720651-49735911	Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases
6	esv12377	chr3:49720751-49735851	Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs11130214	WDR6	cis	multi-tissue	Pritchard
rs11130214	WDR6	cis	Whole Blood	GTEx
rs11130214	CCDC71	cis	cerebellum	SCAN
rs11130214	P4HTM	cis	parietal	SCAN
rs11130214	RBM6	cis	parietal	SCAN
rs11130214	ALS2CL	cis	cerebellum	SCAN
rs11130214	C3orf54	cis	cerebellum	SCAN
rs11130214	WDR6	cis	parietal	SCAN
rs11130214	RNF123	cis	cerebellum	SCAN
rs11130214	AMT	cis	cerebellum	SCAN
rs11130214	UCN2	cis	cerebellum	SCAN
rs11130214	RBM6	cis	Nerve Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49727800-49736200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr3:49727800-49740000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:49727800-49742200	Weak transcription	Small Intestine	intestine
4	chr3:49728000-49736200	Weak transcription	HSMMtube	muscle
5	chr3:49728000-49737000	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:49728000-49738400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:49728000-49738600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr3:49728000-49738600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:49728000-49739200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:49728000-49739200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr3:49728000-49739400	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:49728000-49742600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr3:49728000-49744400	Weak transcription	NH-A	brain
14	chr3:49728000-49748800	Weak transcription	A549	lung
15	chr3:49728400-49736200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:49728400-49753200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr3:49728400-49756600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:49728600-49736200	Weak transcription	HSMM	muscle
19	chr3:49728600-49739400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr3:49728600-49744800	Weak transcription	HMEC	breast
21	chr3:49728600-49750400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr3:49729200-49738200	Weak transcription	Hela-S3	cervix
23	chr3:49729200-49749800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:49729200-49750200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:49729200-49755800	Weak transcription	Right Atrium	heart
26	chr3:49729400-49750200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:49731800-49740800	Strong transcription	Fetal Stomach	stomach
28	chr3:49732200-49755000	Strong transcription	Fetal Intestine Small	intestine
29	chr3:49732400-49739000	Enhancers	Fetal Heart	heart
30	chr3:49733000-49750200	Weak transcription	Psoas Muscle	Psoas
31	chr3:49734200-49736200	Strong transcription	NHEK	skin
32	chr3:49734200-49736600	Strong transcription	Adipose Nuclei	Adipose
33	chr3:49734200-49746000	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr3:49734200-49746000	Strong transcription	Thymus	Thymus
35	chr3:49734200-49746200	Strong transcription	Duodenum Mucosa	Duodenum
36	chr3:49734400-49736000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:49734400-49736000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:49734400-49736000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr3:49734400-49736200	Strong transcription	Right Ventricle	heart
40	chr3:49734400-49736400	Strong transcription	Fetal Lung	lung
41	chr3:49734400-49736400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr3:49734400-49736400	Strong transcription	HepG2	liver
43	chr3:49734400-49736600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:49734400-49740400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:49734400-49740600	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr3:49734400-49740800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr3:49734400-49741200	Strong transcription	Spleen	Spleen
48	chr3:49734400-49744000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:49734400-49744000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr3:49734400-49744200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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