Variant report

Variant	rs490032
Chromosome Location	chr8:102896141-102896142
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:153598533..153600803-chr8:102895391..102897521,2	MCF-7	breast:
2	chr8:102895916..102899783-chr8:102900314..102903177,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160678	Chromatin interaction
ENSG00000189171	Chromatin interaction

Extended variants
information (count: 114 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:109)

rs_ID	r²[population]
rs1144545	0.87[CEU][hapmap];0.83[CHB][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1148496	0.95[CEU][hapmap];0.86[GIH][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes]
rs1148497	0.87[CEU][hapmap]
rs1148498	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1148499	0.87[CEU][hapmap];0.86[GIH][hapmap]
rs1148501	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1264865	0.96[CEU][hapmap];0.86[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs1264866	0.86[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1264930	0.89[GIH][hapmap]
rs1264931	0.80[ASW][hapmap];0.88[CEU][hapmap];0.86[GIH][hapmap];0.96[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1264933	0.89[GIH][hapmap]
rs1264942	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1264948	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1264949	0.80[ASN][1000 genomes]
rs1264952	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1264953	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1264954	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1271946	0.87[EUR][1000 genomes]
rs1313944	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2155939	0.88[CEU][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs2155940	0.83[CEU][hapmap];0.84[AMR][1000 genomes]
rs2155941	0.83[CEU][hapmap];0.84[AMR][1000 genomes]
rs2509895	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs472471	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs472638	0.87[CEU][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap]
rs472963	0.87[CEU][hapmap];0.86[GIH][hapmap]
rs473498	0.96[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs477236	0.91[CEU][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs478069	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs478092	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs478875	1.00[CEU][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs478896	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs478917	0.87[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs479041	0.87[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap]
rs479742	0.96[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs480570	0.87[CEU][hapmap];0.83[CHB][hapmap];0.90[ASN][1000 genomes]
rs480955	0.95[CEU][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs481545	0.87[CEU][hapmap];0.89[CHB][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs482023	0.91[CEU][hapmap];0.94[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs484657	0.93[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs485252	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs485263	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs486196	0.95[CEU][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs486496	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs487863	0.91[CEU][hapmap];0.83[CHB][hapmap];0.87[EUR][1000 genomes]
rs487987	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs488034	0.87[CEU][hapmap]
rs489973	0.87[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap]
rs490096	1.00[CEU][hapmap];0.81[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs490125	0.96[CEU][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs494352	0.82[CEU][hapmap]
rs495636	0.87[CEU][hapmap];0.89[CHB][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs497905	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs502334	0.83[CHB][hapmap];0.90[ASN][1000 genomes]
rs505460	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs506026	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs508386	0.96[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs510524	0.95[CEU][hapmap];0.94[CHB][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs512202	0.93[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs513159	0.80[ASW][hapmap];0.87[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs513472	0.87[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs514057	0.86[EUR][1000 genomes]
rs517868	0.91[CEU][hapmap];0.89[CHB][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs519197	0.87[CEU][hapmap]
rs520880	0.87[CEU][hapmap];0.86[GIH][hapmap]
rs526533	0.96[CEU][hapmap];0.89[CHB][hapmap];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs529684	0.87[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[ASN][1000 genomes]
rs531624	0.87[CEU][hapmap];0.83[CHB][hapmap];0.90[ASN][1000 genomes]
rs534512	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs537941	1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs539663	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs540459	0.87[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs542208	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs543897	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs544821	1.00[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs544928	0.91[CEU][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs549281	0.87[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs550281	0.91[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs551295	0.83[CEU][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap]
rs553463	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs554036	0.96[CEU][hapmap]
rs554945	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs557654	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs558159	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs558772	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs558985	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs561000	0.96[CEU][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs561603	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs562037	0.86[CEU][hapmap]
rs563463	0.87[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs563493	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs564718	1.00[CEU][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs566264	0.95[CEU][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs566315	0.87[CEU][hapmap];0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs566392	0.87[CEU][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap]
rs566501	0.95[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs568194	0.87[CEU][hapmap]
rs569015	0.87[CEU][hapmap];0.94[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs569787	0.85[CEU][hapmap]
rs571673	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs572692	1.00[CEU][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs576173	0.90[ASN][1000 genomes]
rs577756	0.87[CEU][hapmap]
rs578603	0.91[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6991592	0.88[CEU][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap]
rs7828175	0.83[CEU][hapmap]
rs7828516	0.88[CEU][hapmap]
rs7829693	0.83[CEU][hapmap];0.89[GIH][hapmap]
rs7840760	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	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
5	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
rs490032	NCALD	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102883600-102898600	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr8:102884200-102897600	Weak transcription	Left Ventricle	heart
3	chr8:102885400-102900200	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr8:102887600-102897600	Weak transcription	Right Atrium	heart
5	chr8:102888800-102901000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr8:102889000-102897000	Weak transcription	Stomach Mucosa	stomach
7	chr8:102889600-102896600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr8:102889800-102896400	Weak transcription	Fetal Muscle Leg	muscle
9	chr8:102890000-102896200	Weak transcription	Aorta	Aorta
10	chr8:102890400-102898200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr8:102891800-102897600	Weak transcription	Ovary	ovary
12	chr8:102894400-102901200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr8:102895800-102896400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr8:102896000-102896200	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr8:102896000-102896400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr8:102896000-102896600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr8:102896000-102896600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr8:102896000-102896600	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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