Variant report

Variant	rs793439
Chromosome Location	chr3:99637783-99637784
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99633161..99634866-chr3:99636126..99638471,2	MCF-7	breast:
2	chr3:99629219..99631187-chr3:99636036..99638648,2	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10936003	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11711935	0.81[LWK][hapmap];0.90[MKK][hapmap]
rs11719468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12488245	0.81[CEU][hapmap]
rs1287284	0.84[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs13059754	0.84[CEU][hapmap];0.80[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.82[MKK][hapmap]
rs1384062	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs1387647	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs1610509	0.86[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs16841874	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap]
rs1718235	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4577503	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.85[ASN][1000 genomes]
rs4928150	0.84[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4928151	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs4928153	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs4928230	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4928237	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs58704213	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6440967	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs669676	0.83[ASW][hapmap]
rs6788750	0.86[LWK][hapmap];0.94[MKK][hapmap]
rs6802817	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs6806323	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs704571	0.94[JPT][hapmap]
rs704572	1.00[JPT][hapmap]
rs704574	0.86[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs7613864	0.85[ASN][1000 genomes]
rs7649349	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs7650727	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs766778	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs792831	0.94[JPT][hapmap]
rs792833	0.86[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap]
rs792835	0.86[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs792836	0.94[JPT][hapmap]
rs792837	0.94[JPT][hapmap]
rs793437	0.83[ASN][1000 genomes]
rs793443	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs793446	0.84[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs793450	0.88[LWK][hapmap];0.88[MKK][hapmap]
rs793456	0.82[ASN][1000 genomes]
rs793464	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.83[MKK][hapmap];0.85[ASN][1000 genomes]
rs793469	0.88[LWK][hapmap];0.90[MKK][hapmap]
rs793475	0.84[CEU][hapmap];0.83[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs793476	0.87[ASN][1000 genomes]
rs793482	0.82[YRI][hapmap]
rs793483	0.82[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap]
rs793485	0.94[JPT][hapmap]
rs793497	0.90[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs793502	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs796976	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs813218	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs902159	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs923472	0.84[CEU][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs793439	C3orf26	Cis_1M	lymphoblastoid	RTeQTL
rs793439	OR5H6	cis	cerebellum	SCAN
rs793439	SENP7	cis	parietal	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99600800-99638600	Weak transcription	Left Ventricle	heart
2	chr3:99604600-99648200	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99619600-99644400	Weak transcription	Right Ventricle	heart
4	chr3:99620000-99638600	Weak transcription	Small Intestine	intestine
5	chr3:99621200-99638600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr3:99625000-99639400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:99627200-99638600	Weak transcription	K562	blood
8	chr3:99629000-99639400	Weak transcription	HSMM	muscle
9	chr3:99630000-99638200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr3:99630400-99638400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:99630600-99638000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr3:99630600-99638000	Weak transcription	Osteobl	bone
13	chr3:99630600-99638600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:99630600-99638600	Weak transcription	Fetal Muscle Leg	muscle
15	chr3:99630600-99638600	Weak transcription	Pancreas	Pancrea
16	chr3:99630600-99638800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr3:99630600-99644600	Weak transcription	NH-A	brain
18	chr3:99630800-99638400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr3:99631200-99638400	Weak transcription	NHEK	skin
20	chr3:99631400-99638400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr3:99631400-99638600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:99631800-99639800	Weak transcription	Primary B cells from cord blood	blood
23	chr3:99633400-99638600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:99633600-99638400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr3:99633600-99638600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr3:99634000-99638600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:99634400-99647400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr3:99635000-99639800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr3:99635200-99638800	Weak transcription	Liver	Liver
30	chr3:99635800-99638600	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:99637200-99639600	Enhancers	HUVEC	blood vessel
32	chr3:99637200-99641800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr3:99637400-99637800	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr3:99637400-99639000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:99637400-99639200	Enhancers	HepG2	liver
36	chr3:99637400-99640000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr3:99637600-99637800	Enhancers	Fetal Lung	lung
38	chr3:99637600-99638400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:99637600-99638600	Weak transcription	Psoas Muscle	Psoas
40	chr3:99637600-99641000	Enhancers	Adipose Nuclei	Adipose
41	chr3:99637600-99641600	Enhancers	Muscle Satellite Cultured Cells	--

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