Variant report

Variant	rs472638
Chromosome Location	chr8:102879029-102879030
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	chr8:102878636..102880767-chr8:102882100..102885005,2	MCF-7	breast:
2	chr8:102878654..102880299-chr8:102886876..102888668,2	MCF-7	breast:

Extended variants
information (count: 118 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1144545	1.00[CEU][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1148496	0.91[CEU][hapmap];0.94[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs1148497	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1148498	0.87[CEU][hapmap]
rs1148499	0.82[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.83[LWK][hapmap];0.90[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1264865	0.83[CEU][hapmap];0.94[GIH][hapmap];0.80[TSI][hapmap]
rs1264866	0.87[CEU][hapmap];0.92[GIH][hapmap];0.80[TSI][hapmap]
rs1264930	0.87[CEU][hapmap];0.92[GIH][hapmap];0.85[TSI][hapmap]
rs1264931	0.89[GIH][hapmap]
rs1264933	0.92[GIH][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes]
rs1264942	0.84[ASN][1000 genomes]
rs1264946	0.82[EUR][1000 genomes]
rs1264948	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1264949	0.82[EUR][1000 genomes]
rs1271946	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1272384	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1313944	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1313945	0.82[EUR][1000 genomes]
rs2155938	0.87[CEU][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2155939	0.92[GIH][hapmap]
rs2155942	0.83[CEU][hapmap]
rs2226724	0.87[CEU][hapmap]
rs35473722	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs472471	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs472963	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs473498	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs477236	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs478092	0.87[CEU][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];0.83[ASN][1000 genomes]
rs478189	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs478875	0.87[CEU][hapmap]
rs478896	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs478917	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs479041	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs479742	0.83[CEU][hapmap];0.84[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs480570	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs480955	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs481545	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs482023	0.94[ASW][hapmap];0.95[CEU][hapmap];0.89[CHD][hapmap];0.91[LWK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs484657	0.87[CEU][hapmap];0.86[GIH][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes]
rs485252	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs485263	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs485363	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs486196	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs486496	0.80[EUR][1000 genomes]
rs487863	0.95[CEU][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs487987	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs488034	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs489973	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs490032	0.87[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap]
rs490096	0.87[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[ASN][1000 genomes]
rs490125	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs494352	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs495636	1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs497905	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs502334	0.91[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs505460	0.89[ASN][1000 genomes]
rs506026	0.84[ASN][1000 genomes]
rs508386	0.83[CEU][hapmap];0.81[GIH][hapmap]
rs510524	0.83[CEU][hapmap];0.89[CHB][hapmap];0.98[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs512202	0.87[CEU][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.80[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs513159	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs513472	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs514057	0.91[EUR][1000 genomes]
rs517868	0.95[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs519197	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs520880	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs526533	0.91[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs529684	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.98[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];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs531624	1.00[CEU][hapmap];0.90[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs534512	0.87[CEU][hapmap]
rs537941	0.87[CEU][hapmap];0.92[GIH][hapmap];0.85[TSI][hapmap]
rs539663	0.87[CEU][hapmap]
rs540459	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs542208	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs543897	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs544821	0.87[CEU][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs544928	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs549281	1.00[CEU][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs550281	0.95[CEU][hapmap];0.84[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.87[TSI][hapmap];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs551295	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs553463	0.85[ASN][1000 genomes]
rs554036	0.91[CEU][hapmap]
rs554945	0.87[CEU][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs557654	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs558159	0.93[ASN][1000 genomes]
rs558772	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs558985	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs561000	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.95[ASN][1000 genomes]
rs561603	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs562037	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs563463	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs563493	0.87[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs564718	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.80[TSI][hapmap];0.93[ASN][1000 genomes]
rs566264	0.91[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs566315	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs566392	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566501	0.91[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs568194	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569015	1.00[CEU][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs569787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs572692	0.87[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs576173	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs577756	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs578603	0.88[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67887846	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6984260	0.87[CEU][hapmap]
rs6991592	0.92[GIH][hapmap]
rs7813132	0.86[CEU][hapmap]
rs7827941	0.87[CEU][hapmap]
rs7829693	0.92[GIH][hapmap];0.88[TSI][hapmap]
rs9297313	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv1030076	chr8:102866179-102896458	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs472638	NCALD	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102869200-102880200	Weak transcription	Aorta	Aorta
2	chr8:102870000-102891200	Weak transcription	Ovary	ovary
3	chr8:102871000-102880400	Weak transcription	Psoas Muscle	Psoas
4	chr8:102871000-102880800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr8:102876600-102879200	Weak transcription	Fetal Muscle Leg	muscle
6	chr8:102876600-102880400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr8:102876600-102883400	Weak transcription	NHDF-Ad	bronchial
8	chr8:102876800-102879400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr8:102879000-102881000	Enhancers	Small Intestine	intestine
10	chr8:102879000-102881000	Enhancers	Stomach Mucosa	stomach

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