Variant report

Variant	rs9811318
Chromosome Location	chr3:48702606-48702607
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48702385-48702681	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr3:48698903-48702611	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:48702386-48702745	GM12878	blood:	n/a	n/a
4	RCOR1	chr3:48700229-48702805	IMR90	lung:	n/a	n/a
5	POLR2A	chr3:48702465-48702654	K562	blood:	n/a	n/a
6	POLR2A	chr3:48698670-48702902	H1-hESC	embryonic stem cell:	n/a	n/a
7	POLR2A	chr3:48702474-48702704	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr3:48699093-48702773	HepG2	liver:	n/a	n/a
9	POLR2A	chr3:48702582-48702656	GM12878	blood:	n/a	n/a
10	POLR2A	chr3:48702411-48702758	H1-hESC	embryonic stem cell:	n/a	n/a

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48699299..48703873-chr3:48715927..48726939,20	MCF-7	breast:
2	chr3:48698129..48704726-chr3:48706101..48715056,13	MCF-7	breast:
3	chr3:48700180..48704062-chr3:48721751..48723924,3	K562	blood:
4	chr3:48596168..48597991-chr3:48701051..48702925,2	K562	blood:
5	chr3:48680179..48682493-chr3:48699784..48702712,4	MCF-7	breast:
6	chr3:48701214..48702790-chr3:48729713..48732304,2	MCF-7	breast:
7	chr3:48670764..48674544-chr3:48699167..48702803,6	K562	blood:
8	chr3:48670764..48674544-chr3:48698929..48702803,9	K562	blood:
9	chr3:48700630..48703207-chr3:49044613..49046334,2	K562	blood:
10	chr3:48698738..48703197-chr3:48713751..48717809,8	K562	blood:
11	chr3:48701660..48704427-chr3:48712006..48713565,2	K562	blood:
12	chr3:48667529..48675453-chr3:48697968..48703139,10	MCF-7	breast:
13	chr3:48700863..48702620-chr3:48955867..48958209,2	K562	blood:
14	chr3:48701937..48704062-chr3:48721900..48723446,2	K562	blood:
15	chr3:48700103..48702620-chr3:48955233..48957367,3	K562	blood:
16	chr3:48699573..48703813-chr3:48719476..48724654,10	MCF-7	breast:
17	chr3:48669152..48670983-chr3:48700604..48702658,2	MCF-7	breast:

No data

Variant related genes	Relation type
CELSR3	TF binding region
ENSG00000008300	Chromatin interaction
ENSG00000213672	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000263898	Chromatin interaction
ENSG00000271973	Chromatin interaction
ENSG00000068745	Chromatin interaction
ENSG00000177479	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000178252	Chromatin interaction
ENSG00000221883	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1003649	0.83[GIH][hapmap]
rs10470687	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs11557629	0.85[EUR][1000 genomes]
rs11706203	0.82[EUR][1000 genomes]
rs11706983	1.00[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs11708786	1.00[GIH][hapmap]
rs11713694	0.83[GIH][hapmap]
rs11719291	1.00[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs12107252	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12107418	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12493578	0.86[YRI][hapmap]
rs12497850	0.83[YRI][hapmap]
rs12715429	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13060933	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13063223	0.82[EUR][1000 genomes]
rs13063312	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.83[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];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13074318	0.83[GIH][hapmap]
rs13076269	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13090013	0.85[EUR][1000 genomes]
rs13091944	1.00[JPT][hapmap]
rs13096357	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13316551	0.82[EUR][1000 genomes]
rs13319651	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs13324119	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13324142	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13434258	1.00[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs1352420	0.83[ASW][hapmap];0.93[YRI][hapmap]
rs17080289	0.80[CHD][hapmap];1.00[GIH][hapmap]
rs17080319	0.85[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];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2276852	0.82[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2286651	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2286652	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2302295	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2310996	0.88[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2310997	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28452701	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2854394	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs28567949	0.85[EUR][1000 genomes]
rs28657585	0.83[EUR][1000 genomes]
rs34037363	0.83[GIH][hapmap]
rs34096717	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34153629	0.85[EUR][1000 genomes]
rs34368826	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34577723	0.83[EUR][1000 genomes]
rs34638686	0.80[EUR][1000 genomes]
rs35064573	1.00[GIH][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs3733086	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3806694	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821875	0.81[CEU][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3821876	0.90[CEU][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3969942	0.83[GIH][hapmap]
rs4858798	0.83[YRI][hapmap]
rs4858828	0.83[YRI][hapmap]
rs4858831	0.83[YRI][hapmap]
rs57334642	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6768448	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773261	0.90[CEU][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6781283	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs6788650	0.83[ASW][hapmap];0.83[YRI][hapmap]
rs6792156	0.88[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	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6806059	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs73078362	0.82[EUR][1000 genomes]
rs740787	0.83[ASW][hapmap];0.90[CEU][hapmap];0.88[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7428949	1.00[JPT][hapmap]
rs7620853	0.90[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7631574	0.88[ASW][hapmap];0.90[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9809222	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9810549	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9810991	0.83[GIH][hapmap]
rs9811027	0.85[EUR][1000 genomes]
rs9812200	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	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9821797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830581	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs9836462	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];0.83[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9837687	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9841602	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];0.83[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
rs9854034	0.82[EUR][1000 genomes]
rs9868809	0.81[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.81[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];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875911	0.83[GIH][hapmap]
rs9877542	0.82[EUR][1000 genomes]
rs9877685	0.82[EUR][1000 genomes]
rs9878063	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9878950	0.83[GIH][hapmap];1.00[JPT][hapmap]
rs9881877	1.00[GIH][hapmap]
rs9882549	1.00[GIH][hapmap];0.82[EUR][1000 genomes]
rs9882962	0.83[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9811318	WDR6	cis	Esophagus Mucosa	GTEx
rs9811318	WDR6	cis	lung	GTEx
rs9811318	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs9811318	WDR6	cis	Nerve Tibial	GTEx
rs9811318	WDR6	cis	lymphoblastoid	seeQTL
rs9811318	WDR6	cis	Adipose Subcutaneous	GTEx
rs9811318	WDR6	cis	Artery Tibial	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48701200-48721000	Weak transcription	Fetal Brain Male	brain
2	chr3:48701600-48702800	Enhancers	Fetal Heart	heart
3	chr3:48701600-48703200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:48701600-48703200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:48701600-48708200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:48701600-48708400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:48701600-48708400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr3:48701600-48708400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr3:48701600-48708600	Weak transcription	Colonic Mucosa	Colon
10	chr3:48701600-48711000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:48701600-48711000	Weak transcription	Left Ventricle	heart
12	chr3:48701600-48711400	Weak transcription	Aorta	Aorta
13	chr3:48701600-48715400	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:48701600-48716800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr3:48701600-48718000	Weak transcription	NHDF-Ad	bronchial
16	chr3:48701600-48720800	Weak transcription	Right Atrium	heart
17	chr3:48701600-48720800	Weak transcription	HUVEC	blood vessel
18	chr3:48701800-48702800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr3:48701800-48703200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr3:48701800-48708200	Weak transcription	Fetal Brain Female	brain
21	chr3:48701800-48708400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:48701800-48708400	Weak transcription	Brain Hippocampus Middle	brain
23	chr3:48701800-48708600	Weak transcription	Adipose Nuclei	Adipose
24	chr3:48701800-48708600	Weak transcription	Liver	Liver
25	chr3:48701800-48708600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr3:48701800-48708600	Weak transcription	Gastric	stomach
27	chr3:48701800-48708600	Weak transcription	Ovary	ovary
28	chr3:48701800-48709000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:48701800-48711200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:48701800-48711400	Weak transcription	Brain Substantia Nigra	brain
31	chr3:48701800-48711400	Weak transcription	Esophagus	oesophagus
32	chr3:48701800-48711600	Weak transcription	Dnd41	blood
33	chr3:48701800-48712400	Weak transcription	Fetal Thymus	thymus
34	chr3:48701800-48713400	Weak transcription	Pancreas	Pancrea
35	chr3:48701800-48714800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:48701800-48715200	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr3:48701800-48715200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr3:48701800-48715600	Weak transcription	NH-A	brain
39	chr3:48701800-48715800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr3:48701800-48715800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr3:48701800-48716800	Weak transcription	Primary T helper cells PMA-I stimulated	--
42	chr3:48701800-48721400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr3:48702000-48702800	Enhancers	H1 Cell Line	embryonic stem cell
44	chr3:48702000-48702800	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr3:48702000-48702800	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr3:48702000-48703200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:48702000-48703200	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr3:48702000-48703200	Enhancers	Stomach Mucosa	stomach
49	chr3:48702000-48703800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:48702000-48707400	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links