Variant report

Variant	rs796976
Chromosome Location	chr3:99621002-99621003
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99618971..99621795-chr3:99720299..99722726,2	MCF-7	breast:
2	chr3:99613503..99616492-chr3:99619175..99621373,2	K562	blood:
3	chr3:99616272..99618855-chr3:99619104..99622005,3	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10936008	0.82[TSI][hapmap]
rs11719468	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs1287284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13059754	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1384062	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1610509	0.88[JPT][hapmap]
rs16841874	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap]
rs1718235	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2638948	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35422475	0.82[AMR][1000 genomes]
rs4577503	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928150	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[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];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928151	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs4928153	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap]
rs4928230	0.84[CEU][hapmap];0.81[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs4928235	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4928237	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs58704213	0.81[ASN][1000 genomes]
rs6440967	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs6802817	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs6806323	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs704571	0.88[JPT][hapmap]
rs704572	0.92[JPT][hapmap]
rs704574	0.88[JPT][hapmap]
rs7613864	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638900	0.82[TSI][hapmap]
rs7649349	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap]
rs7650727	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs766778	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap]
rs792831	0.88[JPT][hapmap]
rs792835	0.88[JPT][hapmap]
rs792836	0.88[JPT][hapmap]
rs792837	0.88[JPT][hapmap]
rs793437	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793439	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs793440	0.82[TSI][hapmap]
rs793443	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793446	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793456	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793464	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];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs793470	0.82[TSI][hapmap]
rs793474	0.82[TSI][hapmap]
rs793475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs793476	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793483	0.88[JPT][hapmap]
rs793485	0.88[JPT][hapmap]
rs793497	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs793502	0.83[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs793503	0.82[TSI][hapmap]
rs796978	0.82[TSI][hapmap]
rs813218	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs902159	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap]
rs923472	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs796976	SENP7	cis	parietal	SCAN
rs796976	EPHX1	trans	cerebellum	SCAN
rs796976	OR5H6	cis	cerebellum	SCAN
rs796976	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

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	chr3:99616000-99631200	Weak transcription	Primary B cells from cord blood	blood
4	chr3:99616600-99622800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr3:99617200-99623200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:99619000-99621200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr3:99619200-99621400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr3:99619200-99621600	Enhancers	NHLF	lung
9	chr3:99619400-99621200	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr3:99619400-99621200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:99619400-99621200	Enhancers	Fetal Lung	lung
12	chr3:99619400-99621400	Enhancers	Brain Hippocampus Middle	brain
13	chr3:99619400-99621400	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr3:99619400-99621400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr3:99619400-99621600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr3:99619400-99623000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:99619600-99621200	Enhancers	HSMMtube	muscle
18	chr3:99619600-99621400	Enhancers	Liver	Liver
19	chr3:99619600-99621400	Enhancers	Fetal Intestine Small	intestine
20	chr3:99619600-99621400	Enhancers	Stomach Mucosa	stomach
21	chr3:99619600-99621600	Flanking Active TSS	NHEK	skin
22	chr3:99619600-99644400	Weak transcription	Right Ventricle	heart
23	chr3:99619800-99621400	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr3:99619800-99621400	Enhancers	GM12878-XiMat	blood
25	chr3:99619800-99626600	Weak transcription	Psoas Muscle	Psoas
26	chr3:99620000-99624200	Enhancers	Hela-S3	cervix
27	chr3:99620000-99624800	Enhancers	NHDF-Ad	bronchial
28	chr3:99620000-99629800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:99620000-99638600	Weak transcription	Small Intestine	intestine
30	chr3:99620200-99621400	Enhancers	Pancreatic Islets	Pancreatic Islet
31	chr3:99620200-99621800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:99620200-99621800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr3:99620400-99621400	Enhancers	Placenta Amnion	Placenta Amnion
34	chr3:99620400-99621600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:99620400-99621600	Enhancers	Brain Substantia Nigra	brain
36	chr3:99620600-99621200	Enhancers	HMEC	breast
37	chr3:99620600-99621400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
38	chr3:99620600-99621400	Enhancers	Brain Anterior Caudate	brain
39	chr3:99620600-99622000	Enhancers	HepG2	liver
40	chr3:99620600-99623800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:99620600-99624600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:99620800-99621200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:99620800-99621200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:99620800-99621400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:99620800-99621400	Enhancers	A549	lung
46	chr3:99620800-99621600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:99620800-99621600	Enhancers	HSMM	muscle
48	chr3:99620800-99621600	Enhancers	Osteobl	bone
49	chr3:99620800-99621800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr3:99620800-99622000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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