Variant report

Variant	rs3213762
Chromosome Location	chr17:38178627-38178628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:16)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr17:38178620-38178770	HEK293	kidney:	n/a	n/a
2	CTCF	chr17:38178620-38178770	HMEC	breast:	n/a	n/a
3	POLR2A	chr17:38177288-38178792	HUVEC	blood vessel:	n/a	n/a
4	CTCF	chr17:38178620-38178770	NHEK	skin:	n/a	n/a
5	POLR2A	chr17:38177199-38178865	U87	brain:	n/a	n/a
6	POLR2A	chr17:38177199-38178884	U87	brain:	n/a	n/a
7	POLR2A	chr17:38178532-38178688	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr17:38177347-38178768	U87	brain:	n/a	n/a
9	POLR2A	chr17:38177321-38178723	HUVEC	blood vessel:	n/a	n/a
10	POLR2A	chr17:38178339-38178705	K562	blood:	n/a	n/a
11	CTCF	chr17:38178520-38178670	BJ	skin:	n/a	n/a
12	CTCF	chr17:38178540-38178690	GM12871	blood:	n/a	n/a
13	CTCF	chr17:38178580-38178730	HEEpiC	esophagus:	n/a	n/a
14	POLR2A	chr17:38177478-38178718	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr17:38177433-38178644	HUVEC	blood vessel:	n/a	n/a
16	POLR2A	chr17:38177292-38178768	U87	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:38177803..38180808-chr17:38181920..38184987,3	K562	blood:
2	chr17:38175295..38180645-chr17:38181007..38185256,8	MCF-7	breast:
3	chr17:38178218..38182497-chr17:38276428..38279757,5	MCF-7	breast:
4	chr17:38174842..38178903-chr17:38208625..38211251,3	K562	blood:
5	chr17:38178625..38181576-chr17:38444051..38445917,2	K562	blood:
6	chr17:38177907..38180041-chr17:38332919..38334626,2	MCF-7	breast:
7	chr17:38175071..38177613-chr17:38178105..38180812,3	MCF-7	breast:

No data

Variant related genes	Relation type
MED24	TF binding region
ENSG00000094804	Chromatin interaction
ENSG00000188895	Chromatin interaction
ENSG00000238793	Chromatin interaction
ENSG00000008838	Chromatin interaction
ENSG00000108352	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1042658	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1045929	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11078934	0.93[ASW][hapmap];0.84[CEU][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11655264	0.92[YRI][hapmap]
rs11658328	0.85[YRI][hapmap]
rs11871747	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12600856	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12602172	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12941811	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12950335	0.84[ASN][1000 genomes]
rs2227315	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2227322	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2227336	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241245	0.85[YRI][hapmap]
rs2305482	0.85[YRI][hapmap]
rs3826331	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3884477	0.85[ASN][1000 genomes]
rs3935280	0.83[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3936197	0.86[ASN][1000 genomes]
rs4065321	0.85[YRI][hapmap]
rs4794822	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4794823	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4794824	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4795412	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4795414	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4795415	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4795416	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4795418	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4795419	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4795420	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55771023	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55846942	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56922390	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57065891	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57968500	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59925331	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60082402	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62065177	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6503530	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6503533	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7021	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs709591	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs709592	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7208815	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7209755	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7214085	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7221894	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7222039	0.83[ASN][1000 genomes]
rs7502514	0.84[CEU][hapmap];0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7502912	0.89[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7503555	0.83[ASN][1000 genomes]
rs8065443	0.83[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs8065519	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs8066582	0.85[YRI][hapmap]
rs8066846	0.83[ASN][1000 genomes]
rs8067817	0.83[ASN][1000 genomes]
rs8068260	0.80[ASN][1000 genomes]
rs8070454	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8072548	0.83[ASN][1000 genomes]
rs8073254	0.84[YRI][hapmap]
rs8075668	0.89[YRI][hapmap]
rs8078692	0.84[ASN][1000 genomes]
rs8078723	0.86[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8081692	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs868150	0.83[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.85[ASN][1000 genomes]
rs9303283	0.93[ASW][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[ASN][1000 genomes]
rs9303284	0.86[ASN][1000 genomes]
rs9915252	0.85[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492308	chr17:38033039-38204458	Weak transcription Transcr. at gene 5' and 3' Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs3213762	MED24	cis	Whole Blood	GTEx
rs3213762	GSDMB	cis	cerebellum	SCAN
rs3213762	GSDMA	cis	Artery Aorta	GTEx
rs3213762	MED24	cis	Nerve Tibial	GTEx
rs3213762	MED24	cis	Artery Tibial	GTEx
rs3213762	GSDMA	cis	lung	GTEx
rs3213762	GSDMA	cis	Esophagus Muscularis	GTEx
rs3213762	PSMD3	cis	parietal	SCAN
rs3213762	PSMD3	cis	Frontal Cortex	GTEx
rs3213762	MED24	cis	parietal	SCAN
rs3213762	GSDMA	cis	Adipose Subcutaneous	GTEx
rs3213762	GSDMA	cis	Nerve Tibial	GTEx
rs3213762	MED24	cis	Thyroid	GTEx
rs3213762	MED24	cis	cerebellum	SCAN
rs3213762	MED24	cis	Artery Aorta	GTEx
rs3213762	PCGF2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38166800-38181600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr17:38170000-38178800	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr17:38170400-38181600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr17:38171400-38186000	Weak transcription	Small Intestine	intestine
5	chr17:38173000-38179600	Strong transcription	Fetal Intestine Small	intestine
6	chr17:38173000-38181400	Weak transcription	Fetal Kidney	kidney
7	chr17:38173400-38183800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr17:38173400-38192800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr17:38173600-38180200	Genic enhancers	Fetal Muscle Trunk	muscle
10	chr17:38173600-38180400	Genic enhancers	NHLF	lung
11	chr17:38173600-38182000	Strong transcription	Thymus	Thymus
12	chr17:38173800-38179400	Strong transcription	Fetal Intestine Large	intestine
13	chr17:38173800-38179800	Genic enhancers	Spleen	Spleen
14	chr17:38173800-38180600	Strong transcription	Brain Anterior Caudate	brain
15	chr17:38173800-38181400	Strong transcription	Primary T cells fromperipheralblood	blood
16	chr17:38173800-38181800	Strong transcription	Primary T cells from cord blood	blood
17	chr17:38173800-38182400	Strong transcription	Duodenum Mucosa	Duodenum
18	chr17:38174000-38192600	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr17:38174000-38193800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr17:38174200-38179600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr17:38174200-38180400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr17:38174200-38180800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr17:38174200-38183200	Strong transcription	Placenta	Placenta
24	chr17:38174200-38183400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr17:38174200-38183400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr17:38174200-38187400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr17:38174400-38179200	Strong transcription	Pancreas	Pancrea
28	chr17:38174400-38179800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:38174400-38183200	Strong transcription	Primary B cells from peripheral blood	blood
30	chr17:38174400-38193200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr17:38174600-38180400	Genic enhancers	Fetal Muscle Leg	muscle
32	chr17:38174600-38181400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr17:38174600-38181800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr17:38174600-38182000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr17:38174800-38181400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr17:38174800-38192600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr17:38175000-38180600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr17:38175000-38193800	Strong transcription	HepG2	liver
39	chr17:38175200-38181600	Strong transcription	Fetal Thymus	thymus
40	chr17:38175200-38182800	Strong transcription	Brain Angular Gyrus	brain
41	chr17:38175200-38192600	Strong transcription	Fetal Brain Female	brain
42	chr17:38175200-38193200	Strong transcription	Dnd41	blood
43	chr17:38175400-38179800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr17:38175400-38180200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
45	chr17:38175400-38182200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr17:38175400-38188200	Weak transcription	Fetal Heart	heart
47	chr17:38175600-38181800	Weak transcription	Fetal Brain Male	brain
48	chr17:38175600-38191400	Strong transcription	Brain Hippocampus Middle	brain
49	chr17:38175600-38193200	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr17:38175600-38193200	Strong transcription	Brain Cingulate Gyrus	brain

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