Variant report

Variant	rs10112852
Chromosome Location	chr8:90761485-90761486
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	chr8:90760271..90762627-chr8:90995330..90996985,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104320	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1003843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10095743	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12675281	0.80[EUR][1000 genomes]
rs13252013	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13252917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13259882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13279023	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1397308	0.81[CEU][hapmap]
rs16900429	0.81[CHB][hapmap]
rs184302	0.85[EUR][1000 genomes]
rs218895	0.86[EUR][1000 genomes]
rs218899	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs218900	0.96[CEU][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218901	0.96[CEU][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218902	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs218903	0.96[CEU][hapmap]
rs218905	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs218907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs218908	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs218909	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs218910	0.88[EUR][1000 genomes]
rs218913	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs218914	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs218916	0.80[EUR][1000 genomes]
rs218925	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs218929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs218932	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs218934	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs218936	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs218944	0.86[EUR][1000 genomes]
rs218946	0.87[EUR][1000 genomes]
rs218947	0.87[EUR][1000 genomes]
rs218948	0.85[EUR][1000 genomes]
rs2644021	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2644033	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735870	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2735871	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2735873	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735878	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2735882	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs369771	0.82[CHB][hapmap]
rs370282	0.85[AMR][1000 genomes]
rs383592	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs385524	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs394108	0.82[CHB][hapmap]
rs39499	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs39500	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs39503	0.88[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs39504	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs39505	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs39506	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs39509	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs39515	0.82[CHB][hapmap]
rs39761	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs400411	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs40246	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs40247	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs402886	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs40382	0.84[AMR][1000 genomes]
rs40452	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs40453	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs40459	0.81[CEU][hapmap]
rs40544	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs40545	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs40547	0.82[AMR][1000 genomes]
rs405734	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs40636	0.86[AMR][1000 genomes]
rs40638	0.85[AMR][1000 genomes]
rs410663	0.81[CEU][hapmap]
rs411279	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs416324	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs419754	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs42346	0.86[AMR][1000 genomes]
rs42481	0.81[CEU][hapmap]
rs42490	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs431264	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs43134	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs43135	0.83[AMR][1000 genomes]
rs43225	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs447618	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs454441	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs454561	0.82[CHB][hapmap]
rs465	0.84[AMR][1000 genomes]
rs4961158	0.80[EUR][1000 genomes]
rs51331	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6470366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67143546	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6992985	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6993133	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7824932	0.84[EUR][1000 genomes]

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	nsv891180	chr8:90697810-90802491	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
2	nsv933502	chr8:90702392-91049100	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
3	nsv934114	chr8:90720182-90999106	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv891181	chr8:90737258-90819998	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10112852	RP11-37B2.1	cis	Adipose Subcutaneous	GTEx
rs10112852	RP11-37B2.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10112852	RP11-37B2.1	cis	Nerve Tibial	GTEx
rs10112852	RP11-37B2.1	cis	Artery Tibial	GTEx
rs10112852	RP11-37B2.1	cis	Thyroid	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:90741600-90768200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr8:90742600-90767600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr8:90742800-90762200	Weak transcription	Aorta	Aorta
4	chr8:90746200-90767800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr8:90749600-90762200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr8:90749600-90768200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr8:90749800-90767800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr8:90749800-90768000	Weak transcription	Left Ventricle	heart
9	chr8:90749800-90768000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr8:90750000-90769000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr8:90755000-90762400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr8:90755000-90767200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr8:90755200-90766600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr8:90755400-90766400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr8:90755600-90766600	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr8:90756400-90762400	Weak transcription	Fetal Stomach	stomach
17	chr8:90756400-90764000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr8:90756400-90769200	Weak transcription	Pancreas	Pancrea
19	chr8:90758400-90769000	Weak transcription	Ovary	ovary
20	chr8:90759400-90766800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr8:90760000-90768200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr8:90760200-90766400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr8:90760200-90768000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr8:90760400-90766200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr8:90760400-90767800	Weak transcription	Fetal Lung	lung
26	chr8:90760600-90768800	Weak transcription	Fetal Kidney	kidney
27	chr8:90760600-90769000	Weak transcription	HSMM	muscle

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