Variant report

Variant	rs537941
Chromosome Location	chr8:102865222-102865223
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:102864772..102866695-chr8:102870312..102872200,2	MCF-7	breast:

Extended variants
information (count: 111 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1144545	0.87[CEU][hapmap]
rs1148496	0.95[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1148497	0.87[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1148498	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148499	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1148501	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1264865	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1264866	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1264930	0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.90[ASN][1000 genomes]
rs1264931	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1264932	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1264933	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[ASN][1000 genomes]
rs1264948	0.81[EUR][1000 genomes]
rs1264952	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1264953	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1264954	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1271946	0.82[EUR][1000 genomes]
rs1272384	0.94[ASN][1000 genomes]
rs1313944	0.81[EUR][1000 genomes]
rs2155938	0.94[CHB][hapmap];0.94[ASN][1000 genomes]
rs2155939	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2155940	0.83[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs2155941	0.83[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs2509895	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28623673	0.93[ASN][1000 genomes]
rs472471	0.96[CEU][hapmap];0.93[CHB][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs472638	0.87[CEU][hapmap];0.92[GIH][hapmap];0.85[TSI][hapmap]
rs472963	0.87[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs473498	0.96[CEU][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs477236	0.91[CEU][hapmap]
rs478092	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs478875	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs478917	0.87[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs479041	0.87[CEU][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap]
rs479742	0.96[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs480570	0.87[CEU][hapmap]
rs480955	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs481545	0.87[CEU][hapmap]
rs482023	0.91[CEU][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs484657	1.00[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs486196	0.95[CEU][hapmap];0.84[EUR][1000 genomes]
rs486496	0.85[EUR][1000 genomes]
rs487863	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs487987	0.82[EUR][1000 genomes]
rs488034	0.87[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs489973	0.87[CEU][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap]
rs490032	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs490096	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs490125	0.96[CEU][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs494352	0.82[CEU][hapmap]
rs495636	0.87[CEU][hapmap]
rs497905	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs505460	0.82[EUR][1000 genomes]
rs506026	0.89[EUR][1000 genomes]
rs508386	0.96[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs510524	0.95[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs512202	1.00[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs513159	0.87[CEU][hapmap];0.86[TSI][hapmap]
rs513472	0.87[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs514057	0.81[EUR][1000 genomes]
rs517868	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs519197	0.87[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs520880	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.82[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs526533	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs529684	0.87[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap]
rs531624	0.87[CEU][hapmap]
rs534512	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs539663	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs540459	0.87[CEU][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap]
rs543897	0.88[EUR][1000 genomes]
rs544821	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs544928	0.91[CEU][hapmap]
rs549281	0.87[CEU][hapmap];0.86[GIH][hapmap];0.82[TSI][hapmap]
rs550281	0.91[CEU][hapmap];0.86[GIH][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs551295	0.83[CEU][hapmap];0.94[GIH][hapmap];0.85[TSI][hapmap]
rs553463	0.82[EUR][1000 genomes]
rs554036	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs554945	1.00[CEU][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][1000 genomes]
rs557654	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs558159	0.86[EUR][1000 genomes]
rs558985	0.87[EUR][1000 genomes]
rs561000	0.96[CEU][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs561603	0.82[EUR][1000 genomes]
rs562037	0.86[CEU][hapmap]
rs563463	0.87[CEU][hapmap];0.97[GIH][hapmap]
rs563493	1.00[CEU][hapmap]
rs564718	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs566264	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs566315	0.87[CEU][hapmap]
rs566392	0.87[CEU][hapmap];0.97[GIH][hapmap];0.85[TSI][hapmap]
rs566501	0.95[CEU][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs568194	0.87[CEU][hapmap]
rs569015	0.87[CEU][hapmap]
rs569787	0.85[CEU][hapmap]
rs571673	0.83[EUR][1000 genomes]
rs572692	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs577756	0.87[CEU][hapmap]
rs578603	0.91[CEU][hapmap]
rs67887846	0.94[ASN][1000 genomes]
rs6991592	0.88[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7828175	0.83[CEU][hapmap]
rs7828516	0.88[CEU][hapmap]
rs7829693	0.83[CEU][hapmap];1.00[GIH][hapmap]
rs7840760	0.83[CEU][hapmap]
rs9297313	0.94[CHB][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018653	chr8:102818271-103009082	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv539700	chr8:102818271-103009082	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv518162	chr8:102841031-102893626	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv523850	chr8:102841031-102893626	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv465749	chr8:102847202-102929460	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv611819	chr8:102847202-102929460	Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs537941	NCALD	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102803600-102870600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr8:102846800-102866400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr8:102854800-102866200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr8:102859600-102866200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr8:102862400-102869600	Weak transcription	Left Ventricle	heart
6	chr8:102862600-102865800	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr8:102862600-102866000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr8:102862600-102866400	Weak transcription	NHEK	skin
9	chr8:102862600-102866600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr8:102862600-102867000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr8:102862600-102867600	Weak transcription	Right Ventricle	heart
12	chr8:102862600-102868600	Weak transcription	Aorta	Aorta
13	chr8:102862600-102868600	Weak transcription	Ovary	ovary
14	chr8:102862800-102876000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr8:102863000-102865800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr8:102863000-102865800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr8:102864000-102866400	Enhancers	HSMMtube	muscle
18	chr8:102864000-102867600	Enhancers	Fetal Muscle Leg	muscle
19	chr8:102864600-102867400	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr8:102865000-102865800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr8:102865000-102866000	Weak transcription	Psoas Muscle	Psoas
22	chr8:102865000-102866000	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr8:102865000-102866400	Weak transcription	Lung	lung
24	chr8:102865000-102869200	Weak transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links