Variant report

Variant	rs4928150
Chromosome Location	chr3:99685991-99685992
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:99683941..99686099-chr3:99690442..99692720,2	MCF-7	breast:
2	chr3:99592456..99594885-chr3:99685238..99688172,2	MCF-7	breast:
3	chr3:99684840..99686543-chr3:99978018..99980934,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000036054	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10222474	0.86[CEU][hapmap]
rs10936008	0.82[TSI][hapmap]
rs11719468	0.84[CEU][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs12488245	0.96[CEU][hapmap];0.91[GIH][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap]
rs1287284	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13059754	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1384062	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[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];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1387647	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap]
rs16841874	0.84[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap]
rs1718235	0.84[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs2130369	0.88[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs2638948	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35422475	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4577503	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4928153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap]
rs4928230	0.84[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap]
rs4928235	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4928237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58704213	0.85[ASN][1000 genomes]
rs6440967	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6767441	0.92[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]
rs6802817	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs6806323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6808765	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7613864	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7629487	0.92[CEU][hapmap]
rs7636776	0.80[AMR][1000 genomes]
rs7638900	0.82[TSI][hapmap]
rs7649349	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7650727	0.84[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs766778	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs793437	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs793439	0.84[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs793440	0.82[TSI][hapmap]
rs793443	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[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];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793446	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs793456	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs793464	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs793470	0.82[TSI][hapmap]
rs793474	0.82[TSI][hapmap]
rs793475	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs793476	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs793483	0.88[JPT][hapmap]
rs793485	0.88[JPT][hapmap]
rs793497	0.96[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs793502	0.83[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs793503	0.82[TSI][hapmap]
rs796976	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]
rs796978	0.82[TSI][hapmap]
rs813218	0.84[CEU][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs902159	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs923472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs9289981	0.87[CEU][hapmap]
rs9811920	0.92[CEU][hapmap];0.82[GIH][hapmap]
rs9837131	0.92[CEU][hapmap];0.80[GIH][hapmap];0.82[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 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
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	esv3325883	chr3:99684162-99687960	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4928150	EPHX1	trans	cerebellum	SCAN
rs4928150	SENP7	cis	parietal	SCAN
rs4928150	OR5H6	cis	cerebellum	SCAN
rs4928150	C3orf26	cis	multi-tissue	Pritchard

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99657600-99686600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:99671600-99688200	Weak transcription	Primary T cells from cord blood	blood
3	chr3:99677400-99696600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:99677600-99692600	Weak transcription	Fetal Lung	lung
5	chr3:99678800-99691800	Enhancers	Skeletal Muscle Female	skeletal muscle
6	chr3:99679600-99688200	Weak transcription	GM12878-XiMat	blood
7	chr3:99679600-99697000	Weak transcription	Fetal Muscle Trunk	muscle
8	chr3:99683000-99687200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:99683200-99686000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:99683200-99686400	Enhancers	Fetal Intestine Small	intestine
11	chr3:99683400-99687000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:99683400-99687200	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr3:99683600-99688600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:99684200-99686000	Enhancers	Small Intestine	intestine
15	chr3:99684200-99687400	Enhancers	HSMMtube	muscle
16	chr3:99684200-99688600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:99684200-99688800	Enhancers	NHEK	skin
18	chr3:99684400-99686400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr3:99684400-99686400	Enhancers	Fetal Stomach	stomach
20	chr3:99684400-99688600	Enhancers	Psoas Muscle	Psoas
21	chr3:99684600-99686400	Enhancers	Colon Smooth Muscle	Colon
22	chr3:99684800-99686600	Enhancers	Fetal Muscle Leg	muscle
23	chr3:99685000-99686000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:99685000-99686200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr3:99685000-99687000	Enhancers	Rectal Smooth Muscle	rectum
26	chr3:99685200-99686200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:99685400-99686400	Weak transcription	Aorta	Aorta
28	chr3:99685400-99687000	Enhancers	Stomach Mucosa	stomach
29	chr3:99685400-99687200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:99685400-99691400	Weak transcription	Right Atrium	heart
31	chr3:99685600-99686000	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr3:99685600-99686000	Weak transcription	Fetal Intestine Large	intestine
33	chr3:99685600-99686000	Enhancers	Fetal Kidney	kidney
34	chr3:99685600-99686000	Flanking Active TSS	Stomach Smooth Muscle	stomach
35	chr3:99685600-99686400	Enhancers	Adipose Nuclei	Adipose
36	chr3:99685600-99686600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:99685600-99688000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr3:99685800-99686000	Enhancers	HSMM	muscle
39	chr3:99685800-99686000	Enhancers	Osteobl	bone
40	chr3:99685800-99686400	Enhancers	Fetal Heart	heart
41	chr3:99685800-99687000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr3:99685800-99688400	Weak transcription	Left Ventricle	heart
43	chr3:99685800-99688600	Enhancers	HMEC	breast

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