Variant report

Variant	rs11709734
Chromosome Location	chr3:49745235-49745236
allele	A/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	chr3:49745133-49745823	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49744504..49746005-chr3:49749616..49751873,2	K562	blood:
2	chr3:49741563..49745269-chr3:49756251..49759503,3	K562	blood:
3	chr3:49743020..49745371-chr3:49755565..49758428,3	K562	blood:
4	chr3:49744683..49746856-chr3:49748059..49750371,2	MCF-7	breast:

Variant related genes	Relation type
RNF123	TF binding region
ENSG00000176020	Chromatin interaction
ENSG00000164068	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10452032	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs1078341	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs10865956	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs11130207	1.00[ASN][1000 genomes]
rs11130208	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs11130211	0.94[CEU][hapmap]
rs11130217	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11720705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12583	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs12637313	0.88[CEU][hapmap];1.00[CHD][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs12715437	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13096480	1.00[ASN][1000 genomes]
rs13322887	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs1352889	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs1463728	1.00[ASN][1000 genomes]
rs1491983	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs1491985	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1532204	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs1586827	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs1799844	0.94[EUR][1000 genomes]
rs1982861	1.00[CHD][hapmap]
rs1996663	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1996664	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2029591	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs2131108	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs2312462	1.00[CHD][hapmap]
rs2329021	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs28535523	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3020779	1.00[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34890793	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap]
rs35129566	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3905330	1.00[CHD][hapmap]
rs4241405	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs4241407	1.00[CHD][hapmap]
rs4855833	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs4855845	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs4855846	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs4855848	1.00[ASN][1000 genomes]
rs4855849	1.00[ASN][1000 genomes]
rs4855853	1.00[ASN][1000 genomes]
rs4855882	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4855885	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs55997059	0.94[EUR][1000 genomes]
rs58339610	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs59357103	0.92[EUR][1000 genomes]
rs59684465	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61557789	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62259933	1.00[ASN][1000 genomes]
rs62260663	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62260720	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62260723	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62261249	1.00[ASN][1000 genomes]
rs62262672	1.00[ASN][1000 genomes]
rs62262673	1.00[ASN][1000 genomes]
rs62262675	1.00[ASN][1000 genomes]
rs62262722	0.99[EUR][1000 genomes]
rs62262730	0.96[EUR][1000 genomes]
rs6446275	1.00[ASN][1000 genomes]
rs6446285	0.94[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[ASN][1000 genomes]
rs6446286	1.00[ASN][1000 genomes]
rs6774202	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs6790568	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6797299	0.94[CEU][hapmap];1.00[ASN][1000 genomes]
rs6804970	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6805609	1.00[ASN][1000 genomes]
rs6809879	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs72934271	1.00[ASN][1000 genomes]
rs7355800	1.00[ASN][1000 genomes]
rs7613491	1.00[ASN][1000 genomes]
rs7613603	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7620848	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7621797	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7628207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7637711	1.00[CEU][hapmap];1.00[CHD][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7644148	1.00[CHD][hapmap]
rs7647973	1.00[ASN][1000 genomes]
rs7649428	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7651372	1.00[ASN][1000 genomes]
rs8897	1.00[ASN][1000 genomes]
rs9824435	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs9829155	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9830730	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs9835157	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9836756	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9849038	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9851651	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9860055	1.00[ASN][1000 genomes]
rs9862534	1.00[CHD][hapmap]
rs9870755	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9870858	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9871024	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs9883000	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv1796605	chr3:49744556-49760567	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs11709734	WDR6	cis	cerebellum	SCAN
rs11709734	DALRD3	cis	parietal	SCAN
rs11709734	OR9G4	trans	parietal	SCAN
rs11709734	ZNF589	cis	parietal	SCAN
rs11709734	AMT	cis	lung	GTEx
rs11709734	GNL3	cis	cerebellum	SCAN
rs11709734	AMT	cis	parietal	SCAN
rs11709734	GMPPB	cis	parietal	SCAN
rs11709734	RBM6	cis	cerebellum	SCAN
rs11709734	RNF123	cis	parietal	SCAN
rs11709734	RNF123	cis	Artery Tibial	GTEx
rs11709734	DALRD3	cis	cerebellum	SCAN
rs11709734	AMT	cis	Thyroid	GTEx
rs11709734	P4HTM	cis	parietal	SCAN
rs11709734	ITIH3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49728000-49748800	Weak transcription	A549	lung
2	chr3:49728400-49753200	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:49728400-49756600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:49728600-49750400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:49729200-49749800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:49729200-49750200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr3:49729200-49755800	Weak transcription	Right Atrium	heart
8	chr3:49729400-49750200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr3:49732200-49755000	Strong transcription	Fetal Intestine Small	intestine
10	chr3:49733000-49750200	Weak transcription	Psoas Muscle	Psoas
11	chr3:49734200-49746000	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:49734200-49746000	Strong transcription	Thymus	Thymus
13	chr3:49734200-49746200	Strong transcription	Duodenum Mucosa	Duodenum
14	chr3:49734400-49745400	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr3:49734400-49745400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:49734400-49746000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:49734400-49746000	Strong transcription	Fetal Intestine Large	intestine
18	chr3:49734400-49746200	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr3:49734400-49746200	Strong transcription	Stomach Smooth Muscle	stomach
20	chr3:49734400-49746200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr3:49734400-49746400	Strong transcription	Brain Hippocampus Middle	brain
22	chr3:49734400-49756000	Strong transcription	Liver	Liver
23	chr3:49734600-49745400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr3:49734600-49745400	Strong transcription	Brain Germinal Matrix	brain
25	chr3:49734600-49746000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr3:49734600-49746200	Strong transcription	Fetal Muscle Leg	muscle
27	chr3:49734600-49746400	Strong transcription	Fetal Thymus	thymus
28	chr3:49734800-49745400	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:49734800-49746200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:49734800-49746200	Strong transcription	Brain Anterior Caudate	brain
31	chr3:49735400-49755400	Weak transcription	Stomach Mucosa	stomach
32	chr3:49736000-49749800	Weak transcription	GM12878-XiMat	blood
33	chr3:49736000-49753000	Weak transcription	K562	blood
34	chr3:49736600-49746000	Strong transcription	Right Ventricle	heart
35	chr3:49736800-49756400	Weak transcription	HSMM	muscle
36	chr3:49737200-49746000	Strong transcription	Ovary	ovary
37	chr3:49737200-49746200	Strong transcription	Adipose Nuclei	Adipose
38	chr3:49739000-49752000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr3:49739000-49756400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr3:49739200-49753200	Weak transcription	Colon Smooth Muscle	Colon
41	chr3:49739400-49746000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:49740000-49755600	Weak transcription	Fetal Brain Male	brain
43	chr3:49740200-49756000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr3:49740200-49756600	Weak transcription	HSMMtube	muscle
45	chr3:49740400-49747400	Weak transcription	Primary hematopoietic stem cells	blood
46	chr3:49740400-49755000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr3:49740600-49759800	Weak transcription	Hela-S3	cervix
48	chr3:49740800-49756400	Weak transcription	Osteobl	bone
49	chr3:49741200-49745400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:49741200-49746800	Strong transcription	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links