Variant report

Variant	rs7650727
Chromosome Location	chr3:99688976-99688977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99683725..99685720-chr3:99687425..99689237,2	MCF-7	breast:

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10936003	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11711935	0.87[MKK][hapmap]
rs11719468	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12488245	0.81[CEU][hapmap]
rs1287284	0.84[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap]
rs13059754	0.84[CEU][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs1384062	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs1387647	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs16841874	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1718235	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4577503	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs4928150	0.84[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs4928151	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap]
rs4928153	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs4928230	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[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];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4928237	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap]
rs58704213	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440967	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs6788750	0.91[MKK][hapmap]
rs6802817	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs6806323	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs7613864	0.81[ASN][1000 genomes]
rs7619512	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7649349	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs766778	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs793439	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]
rs793443	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs793446	0.84[CEU][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs793450	0.82[LWK][hapmap];0.85[MKK][hapmap]
rs793464	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.80[MKK][hapmap];0.81[ASN][1000 genomes]
rs793469	0.82[LWK][hapmap];0.88[MKK][hapmap]
rs793475	0.84[CEU][hapmap];0.93[JPT][hapmap]
rs793476	0.81[ASN][1000 genomes]
rs793482	0.82[YRI][hapmap]
rs793483	0.82[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap]
rs793485	0.94[JPT][hapmap]
rs793497	0.87[CHD][hapmap];0.94[JPT][hapmap]
rs793502	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs796976	0.84[CEU][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs813218	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs902159	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs923472	0.84[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7650727	SENP7	cis	parietal	SCAN
rs7650727	OR5H6	cis	cerebellum	SCAN
rs7650727	C3orf26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99677400-99696600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr3:99677600-99692600	Weak transcription	Fetal Lung	lung
3	chr3:99678800-99691800	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr3:99679600-99697000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr3:99685400-99691400	Weak transcription	Right Atrium	heart
6	chr3:99686000-99690400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr3:99686400-99689600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:99686400-99691200	Weak transcription	Fetal Stomach	stomach
9	chr3:99686400-99691400	Weak transcription	Colon Smooth Muscle	Colon
10	chr3:99686400-99691800	Weak transcription	Fetal Intestine Small	intestine
11	chr3:99686600-99691200	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:99686600-99691200	Weak transcription	Stomach Smooth Muscle	stomach
13	chr3:99686600-99693400	Weak transcription	Placenta	Placenta
14	chr3:99687000-99691200	Weak transcription	HSMM	muscle
15	chr3:99687000-99691400	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr3:99687000-99691400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:99687000-99693000	Weak transcription	Stomach Mucosa	stomach
18	chr3:99687200-99689200	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:99687200-99689600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:99687200-99690600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:99687200-99695200	Weak transcription	Primary B cells from cord blood	blood
22	chr3:99687400-99689400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:99688000-99689200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:99688200-99689200	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr3:99688200-99689800	Enhancers	Primary T cells from cord blood	blood
26	chr3:99688400-99689600	Flanking Active TSS	GM12878-XiMat	blood
27	chr3:99688600-99689800	Weak transcription	Psoas Muscle	Psoas
28	chr3:99688600-99690200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:99688600-99690400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:99688600-99694200	Weak transcription	Left Ventricle	heart
31	chr3:99688800-99690200	Weak transcription	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links