Variant report

Variant	rs479742
Chromosome Location	chr8:102889145-102889146
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:102886318..102888246-chr8:102888335..102890712,2	MCF-7	breast:
2	chr8:102843199..102845818-chr8:102888680..102891293,2	MCF-7	breast:
3	chr8:102503238..102506028-chr8:102887232..102889960,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000254024	Chromatin interaction
ENSG00000083307	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1144545	0.83[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1148496	0.91[CEU][hapmap]
rs1148497	0.83[CEU][hapmap]
rs1148498	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs1148499	0.83[CEU][hapmap]
rs1148501	0.83[EUR][1000 genomes]
rs1264865	0.91[CEU][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs1264866	0.96[CEU][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs1264931	0.83[CEU][hapmap];0.81[TSI][hapmap]
rs1264942	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1264946	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1264948	0.88[EUR][1000 genomes]
rs1264949	0.80[EUR][1000 genomes]
rs1264952	0.80[EUR][1000 genomes]
rs1264954	0.82[EUR][1000 genomes]
rs1271946	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1313944	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1313945	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2155939	0.83[CEU][hapmap];0.86[TSI][hapmap]
rs472471	0.91[CEU][hapmap]
rs472638	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]
rs472963	0.83[CEU][hapmap]
rs473498	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs477236	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs478092	0.96[CEU][hapmap];0.84[CHD][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs478189	0.90[ASN][1000 genomes]
rs478875	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs478896	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs478917	0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs479041	0.83[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs480570	0.83[CEU][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs480955	0.91[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs481545	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs482023	0.87[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs484657	0.96[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes]
rs485252	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs485263	0.82[EUR][1000 genomes]
rs485363	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs486196	0.91[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs486496	0.91[EUR][1000 genomes]
rs487863	0.87[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs487987	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs488034	0.83[CEU][hapmap]
rs489973	0.83[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs490032	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]
rs490096	0.96[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs490125	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs494352	0.83[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs495636	0.83[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs497905	0.91[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs502334	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs505460	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs506026	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs508386	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs510524	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512202	0.96[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs513159	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]
rs513472	0.83[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs514057	0.87[EUR][1000 genomes]
rs517868	0.87[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs519197	0.83[CEU][hapmap]
rs520880	0.83[CEU][hapmap]
rs526533	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs529684	0.83[CEU][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.82[MEX][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs531624	0.83[CEU][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs534512	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs537941	0.96[CEU][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs539663	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs540459	0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.82[MEX][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs542208	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs543897	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs544821	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs544928	0.96[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs549281	0.83[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs550281	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.86[TSI][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs551295	0.84[CHB][hapmap];0.95[CHD][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs553463	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs554036	0.91[CEU][hapmap]
rs554945	0.96[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs557654	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs558159	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs558772	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs558985	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs561000	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs561603	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs562037	0.82[CEU][hapmap];0.84[CHB][hapmap];0.89[ASN][1000 genomes]
rs563463	0.83[CEU][hapmap];0.84[CHB][hapmap];0.91[CHD][hapmap];0.88[ASN][1000 genomes]
rs563493	0.96[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap]
rs564718	0.96[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs566264	0.91[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs566315	0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs566392	0.83[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.81[JPT][hapmap];0.82[MEX][hapmap];0.90[ASN][1000 genomes]
rs566501	0.91[CEU][hapmap];0.84[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs568194	0.83[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs569015	0.83[CEU][hapmap];0.84[CHB][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs569787	0.81[CEU][hapmap];0.80[CHB][hapmap];0.90[ASN][1000 genomes]
rs571673	0.84[CHB][hapmap];0.81[JPT][hapmap];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs572692	0.95[CEU][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs576173	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs577756	0.83[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs578603	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6991592	0.83[CEU][hapmap];0.86[TSI][hapmap]
rs7828516	0.83[CEU][hapmap]

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
rs479742	NCALD	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102870000-102891200	Weak transcription	Ovary	ovary
2	chr8:102881800-102891000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr8:102882800-102889800	Enhancers	Fetal Muscle Leg	muscle
4	chr8:102883600-102898600	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr8:102884200-102897600	Weak transcription	Left Ventricle	heart
6	chr8:102885400-102900200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr8:102886000-102889600	Weak transcription	Aorta	Aorta
8	chr8:102886800-102894000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr8:102887400-102889200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr8:102887600-102897600	Weak transcription	Right Atrium	heart
11	chr8:102888000-102889800	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr8:102888200-102889200	Enhancers	Brain Cingulate Gyrus	brain
13	chr8:102888200-102889800	Enhancers	Brain Substantia Nigra	brain
14	chr8:102888200-102890000	Enhancers	Brain Angular Gyrus	brain
15	chr8:102888400-102889200	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr8:102888400-102890000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr8:102888400-102890000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr8:102888800-102901000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr8:102889000-102897000	Weak transcription	Stomach Mucosa	stomach

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