Variant report

Variant	rs513159
Chromosome Location	chr8:102899476-102899477
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	chr8:102895916..102899783-chr8:102900314..102903177,4	MCF-7	breast:

Extended variants
information (count: 103 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs1144545	0.91[CEU][hapmap];0.84[CHB][hapmap];0.86[EUR][1000 genomes]
rs1148496	0.82[CEU][hapmap]
rs1148497	0.91[CEU][hapmap]
rs1148498	0.87[CEU][hapmap]
rs1148499	0.91[CEU][hapmap]
rs1264865	0.83[CEU][hapmap]
rs1264866	0.81[ASW][hapmap];0.87[CEU][hapmap];0.80[TSI][hapmap]
rs1264942	0.82[EUR][1000 genomes]
rs1264946	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1264948	0.94[EUR][1000 genomes]
rs1264949	0.86[EUR][1000 genomes]
rs1271946	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1313944	0.80[EUR][1000 genomes]
rs1313945	0.92[EUR][1000 genomes]
rs2155939	0.83[TSI][hapmap]
rs2155942	0.83[CEU][hapmap]
rs472471	0.82[CEU][hapmap]
rs472638	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs472963	0.91[CEU][hapmap]
rs473498	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs477236	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs478092	0.87[CEU][hapmap];0.86[CHD][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs478189	0.83[EUR][1000 genomes]
rs478875	0.87[CEU][hapmap]
rs478896	0.83[EUR][1000 genomes]
rs478917	0.91[CEU][hapmap];0.82[GIH][hapmap];0.86[EUR][1000 genomes]
rs479041	0.91[CEU][hapmap];0.82[CHD][hapmap];0.81[EUR][1000 genomes]
rs479742	0.91[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs480570	0.91[CEU][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs480955	0.82[CEU][hapmap]
rs481545	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs482023	0.95[CEU][hapmap];0.94[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs484657	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs485252	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs485263	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs485363	0.85[EUR][1000 genomes]
rs486196	0.82[CEU][hapmap]
rs486496	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs487863	0.95[CEU][hapmap];0.84[CHB][hapmap];0.93[EUR][1000 genomes]
rs487987	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs488034	0.91[CEU][hapmap]
rs489973	0.91[CEU][hapmap];0.82[CHD][hapmap];0.83[EUR][1000 genomes]
rs490032	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]
rs490096	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs490125	0.91[CEU][hapmap];0.82[CHD][hapmap];0.82[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs494352	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs495636	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs497905	0.82[CEU][hapmap]
rs502334	0.83[CEU][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs505460	0.89[EUR][1000 genomes]
rs506026	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs508386	0.91[CEU][hapmap];1.00[GIH][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs510524	0.91[CEU][hapmap];0.83[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs512202	0.87[ASW][hapmap];0.87[CEU][hapmap];0.84[CHB][hapmap];0.80[CHD][hapmap];0.85[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs513472	0.91[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs514057	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs517868	0.95[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs519197	0.91[CEU][hapmap]
rs520880	0.91[CEU][hapmap]
rs526533	0.82[CEU][hapmap]
rs529684	0.91[CEU][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs531624	0.91[CEU][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs534512	0.87[CEU][hapmap]
rs537941	0.87[CEU][hapmap];0.86[TSI][hapmap]
rs539663	0.87[CEU][hapmap]
rs540459	0.91[CEU][hapmap];0.82[GIH][hapmap];0.80[TSI][hapmap];0.86[EUR][1000 genomes]
rs542208	0.94[EUR][1000 genomes]
rs543897	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs544821	0.87[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs544928	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs549281	0.91[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs550281	0.95[CEU][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs551295	0.87[CEU][hapmap];0.82[CHD][hapmap];0.84[EUR][1000 genomes]
rs553463	0.82[EUR][1000 genomes]
rs554036	0.82[CEU][hapmap]
rs554945	0.87[CEU][hapmap];0.94[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.83[TSI][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs557654	0.88[EUR][1000 genomes]
rs558159	0.85[EUR][1000 genomes]
rs558985	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs561000	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs561603	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs562037	0.90[CEU][hapmap]
rs563463	0.91[CEU][hapmap]
rs563493	0.87[CEU][hapmap]
rs564718	0.87[CEU][hapmap];0.80[CHD][hapmap];0.82[EUR][1000 genomes]
rs566264	0.82[CEU][hapmap]
rs566315	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs566392	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs566501	0.82[CEU][hapmap]
rs568194	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs569015	0.91[CEU][hapmap];0.94[CHB][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs569787	0.90[CEU][hapmap];0.83[EUR][1000 genomes]
rs571673	0.94[CHB][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs572692	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs576173	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs577756	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs578603	0.87[CEU][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs6991592	0.83[TSI][hapmap]
rs7813132	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs513159	NCALD	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102885400-102900200	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr8:102888800-102901000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr8:102894400-102901200	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr8:102896400-102914800	Weak transcription	Right Ventricle	heart
5	chr8:102896600-102900000	Weak transcription	K562	blood
6	chr8:102897400-102899600	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr8:102897600-102899600	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr8:102897600-102899600	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr8:102897600-102899600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr8:102897600-102899800	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr8:102897600-102903600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr8:102897800-102900400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr8:102898000-102900200	Weak transcription	Psoas Muscle	Psoas
14	chr8:102898000-102900400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr8:102898000-102901400	Weak transcription	Right Atrium	heart
16	chr8:102898000-102914600	Weak transcription	Ovary	ovary
17	chr8:102898200-102899600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr8:102898200-102899800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr8:102898200-102899800	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr8:102898400-102899600	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr8:102898400-102902600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr8:102898600-102899600	Enhancers	Primary T cells from cord blood	blood
23	chr8:102898600-102899800	Enhancers	Primary T cells fromperipheralblood	blood
24	chr8:102898800-102899800	Enhancers	H1 Cell Line	embryonic stem cell
25	chr8:102898800-102900800	Weak transcription	Stomach Mucosa	stomach
26	chr8:102898800-102902600	Weak transcription	Small Intestine	intestine
27	chr8:102898800-102903200	Weak transcription	NHEK	skin
28	chr8:102899000-102899800	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr8:102899000-102903000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr8:102899200-102899600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr8:102899200-102899600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr8:102899200-102899600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr8:102899200-102899600	Active TSS	Left Ventricle	heart
34	chr8:102899200-102901600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
35	chr8:102899200-102902000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr8:102899400-102899600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
37	chr8:102899400-102899600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr8:102899400-102899800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr8:102899400-102899800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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