Variant report

Variant	rs5030795
Chromosome Location	chr3:49141116-49141117
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:49140983-49141116	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:49141037-49141157	HUVEC	blood vessel:	n/a	n/a
3	MXI1	chr3:49141032-49142989	SK-N-SH	brain:	n/a	chr3:49142594-49142609 chr3:49142596-49142611
4	STAT5A	chr3:49141113-49142771	GM12878	blood:	n/a	n/a
5	POLR2A	chr3:49140962-49142862	K562	blood:	n/a	n/a
6	POLR2A	chr3:49141030-49144468	K562	blood:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:49137934..49140259-chr3:49140747..49142873,2	MCF-7	breast:
2	chr3:49058000..49061504-chr3:49138702..49143374,6	K562	blood:
3	chr3:49062158..49068430-chr3:49139884..49143886,7	K562	blood:
4	chr3:49063558..49068659-chr3:49135988..49142189,8	MCF-7	breast:
5	chr3:49065644..49068081-chr3:49140753..49143557,2	MCF-7	breast:
6	chr3:49130473..49134563-chr3:49139987..49143694,13	MCF-7	breast:
7	chr3:49061676..49064555-chr3:49141091..49142830,2	MCF-7	breast:
8	chr3:49128213..49133667-chr3:49140039..49144982,11	MCF-7	breast:
9	chr3:49064550..49068051-chr3:49140813..49143886,3	K562	blood:
10	chr3:49140491..49143701-chr3:49201484..49205334,5	K562	blood:
11	chr3:49135631..49137925-chr3:49140087..49143203,4	MCF-7	breast:
12	chr3:49140554..49145107-chr3:49167346..49172356,7	MCF-7	breast:
13	chr3:49140522..49142254-chr3:49155638..49159426,3	MCF-7	breast:
14	chr3:49057287..49061253-chr3:49140682..49142501,4	MCF-7	breast:
15	chr3:49130342..49133374-chr3:49140037..49144249,8	K562	blood:
16	chr3:49130019..49133719-chr3:49139545..49142279,6	K562	blood:

No data

Variant related genes	Relation type
QARS	TF binding region
ENSG00000207605	Chromatin interaction
ENSG00000178035	Chromatin interaction
ENSG00000272434	Chromatin interaction
ENSG00000172053	Chromatin interaction
ENSG00000198218	Chromatin interaction
ENSG00000178057	Chromatin interaction
ENSG00000199032	Chromatin interaction
ENSG00000172046	Chromatin interaction
ENSG00000178149	Chromatin interaction
ENSG00000172037	Chromatin interaction
ENSG00000177352	Chromatin interaction

Extended variants
information (count: 131 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs10049462	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10154895	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10865954	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11130184	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1134043	0.93[CEU][hapmap]
rs1134591	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs11552724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11706052	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];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11706189	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11710247	0.94[EUR][1000 genomes]
rs11712006	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11713297	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11715581	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11716334	0.82[ASN][1000 genomes]
rs11716614	0.92[CEU][hapmap];0.81[AMR][1000 genomes]
rs11717978	0.81[EUR][1000 genomes]
rs11718982	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11719220	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11719457	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11720460	0.91[EUR][1000 genomes]
rs11920267	1.00[JPT][hapmap]
rs12487580	0.80[ASN][1000 genomes]
rs12490393	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12493001	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs12629759	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12631989	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12636030	0.89[ASN][1000 genomes]
rs12637037	0.80[ASN][1000 genomes]
rs12637576	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12715434	0.91[EUR][1000 genomes]
rs13064784	0.95[ASN][1000 genomes]
rs13068038	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs13072554	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13077498	1.00[CEU][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs13080725	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13086240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13087930	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];0.85[EUR][1000 genomes]
rs13090839	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13092715	1.00[JPT][hapmap]
rs13096406	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13315711	1.00[JPT][hapmap]
rs2117938	1.00[JPT][hapmap]
rs2304442	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs3212	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs34326553	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34343820	0.86[EUR][1000 genomes]
rs34477108	0.80[EUR][1000 genomes]
rs34504524	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34509487	0.85[EUR][1000 genomes]
rs34566463	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs34580506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34784192	0.91[EUR][1000 genomes]
rs34889065	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35060561	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs35102816	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35108630	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35174559	0.87[CHD][hapmap];1.00[JPT][hapmap]
rs35185152	0.91[EUR][1000 genomes]
rs35283189	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];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35673421	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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3923475	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4279134	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4308307	0.82[ASN][1000 genomes]
rs4364202	0.93[ASN][1000 genomes]
rs4499638	0.87[ASN][1000 genomes]
rs4513485	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4521268	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4536858	0.87[ASN][1000 genomes]
rs4955410	1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs4955418	0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4955419	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4955420	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4955432	1.00[JPT][hapmap]
rs4974078	0.87[CHD][hapmap]
rs4974080	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4974082	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs55713230	0.87[ASN][1000 genomes]
rs55921200	0.85[AMR][1000 genomes]
rs56004653	0.81[AMR][1000 genomes]
rs56306491	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56318350	0.85[EUR][1000 genomes]
rs61583136	0.85[ASN][1000 genomes]
rs61729488	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62262517	0.93[ASN][1000 genomes]
rs6414613	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6446196	1.00[CHB][hapmap]
rs6446205	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs66991555	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67286839	0.91[EUR][1000 genomes]
rs6770112	0.85[ASN][1000 genomes]
rs6779394	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6781790	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs67831908	0.86[EUR][1000 genomes]
rs6784111	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6790914	0.87[ASN][1000 genomes]
rs6794924	0.82[ASN][1000 genomes]
rs6795025	0.87[ASN][1000 genomes]
rs71324929	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71324939	0.91[EUR][1000 genomes]
rs73082362	0.81[AMR][1000 genomes]
rs73084135	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7430198	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7432989	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7615235	0.87[ASN][1000 genomes]
rs7621015	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7626445	1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7628719	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7643368	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7652746	1.00[JPT][hapmap]
rs9311439	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9637481	1.00[JPT][hapmap]
rs9814987	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9826525	0.91[EUR][1000 genomes]
rs9828310	0.91[EUR][1000 genomes]
rs9835439	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9837237	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9837625	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9840050	1.00[CHD][hapmap];0.95[ASN][1000 genomes]
rs9846123	1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs9847839	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs9850134	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9850917	1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs9855123	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9862483	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9880088	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9880309	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs9884022	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9990153	1.00[CEU][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876764	chr3:49040462-49245645	Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	279 gene(s)	inside rSNPs	diseases
2	nsv834686	chr3:49106047-49270556	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
3	nsv876765	chr3:49119063-49160671	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs5030795	WDR6	cis	Adipose Subcutaneous	GTEx
rs5030795	USP4	cis	multi-tissue	Pritchard
rs5030795	WDR6	cis	Esophagus Mucosa	GTEx
rs5030795	WDR6	cis	Artery Tibial	GTEx
rs5030795	WDR6	cis	multi-tissue	Pritchard
rs5030795	WDR6	cis	Skin Sun Exposed Lower leg	GTEx
rs5030795	WDR6	cis	Whole Blood	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49132400-49141600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:49133200-49141200	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr3:49133600-49141400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:49139000-49141400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr3:49140000-49141200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr3:49140000-49141200	Weak transcription	Ovary	ovary
7	chr3:49140000-49141200	Weak transcription	HSMMtube	muscle
8	chr3:49140000-49141400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:49140000-49141400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:49140000-49141600	Weak transcription	Aorta	Aorta
11	chr3:49140200-49141200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr3:49140200-49141200	Weak transcription	Fetal Kidney	kidney
13	chr3:49140600-49141200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:49140600-49141200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:49140600-49141200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:49140600-49141200	Enhancers	Primary T cells fromperipheralblood	blood
17	chr3:49140600-49141200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr3:49140600-49141200	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr3:49140600-49141200	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr3:49140600-49141200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:49140600-49141200	Genic enhancers	Fetal Brain Female	brain
22	chr3:49140600-49141200	Enhancers	Fetal Heart	heart
23	chr3:49140600-49141200	Genic enhancers	Fetal Intestine Large	intestine
24	chr3:49140600-49141200	Genic enhancers	Fetal Muscle Leg	muscle
25	chr3:49140600-49141200	Genic enhancers	Fetal Thymus	thymus
26	chr3:49140600-49141200	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
27	chr3:49140600-49141400	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr3:49140600-49141400	Enhancers	Esophagus	oesophagus
29	chr3:49140600-49141400	Enhancers	Lung	lung
30	chr3:49140600-49142000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
31	chr3:49140600-49142200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr3:49140800-49141200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:49140800-49141200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:49140800-49141200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:49140800-49141200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr3:49140800-49141200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr3:49140800-49141200	Enhancers	Liver	Liver
38	chr3:49140800-49141200	Genic enhancers	Brain Anterior Caudate	brain
39	chr3:49140800-49141200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr3:49140800-49141200	Enhancers	Brain Substantia Nigra	brain
41	chr3:49140800-49141200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr3:49140800-49141200	Genic enhancers	Fetal Intestine Small	intestine
43	chr3:49140800-49141200	Genic enhancers	Fetal Stomach	stomach
44	chr3:49140800-49141200	Enhancers	Left Ventricle	heart
45	chr3:49140800-49141200	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr3:49140800-49141200	Enhancers	Right Atrium	heart
47	chr3:49140800-49141200	Enhancers	Stomach Mucosa	stomach
48	chr3:49140800-49141200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
49	chr3:49140800-49141200	Enhancers	NHDF-Ad	bronchial
50	chr3:49140800-49141400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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