Variant report

Variant	rs3735513
Chromosome Location	chr7:83631376-83631377
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	chr7:83628708..83631589-chr7:83641659..83643876,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10250165	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10250543	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253563	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10253580	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10261519	0.82[EUR][1000 genomes]
rs10499878	0.88[MEX][hapmap]
rs11978893	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979659	0.93[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13241380	0.87[CEU][hapmap];0.85[CHB][hapmap];0.99[EUR][1000 genomes]
rs1404477	0.88[MEX][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs1404478	0.82[EUR][1000 genomes]
rs1404479	0.99[EUR][1000 genomes]
rs1404480	0.91[TSI][hapmap];0.82[EUR][1000 genomes]
rs2030679	0.87[CEU][hapmap];0.85[CHB][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2527040	0.96[CHD][hapmap]
rs3735514	0.93[CEU][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3735515	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801597	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801598	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801599	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.86[TSI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801600	0.88[MEX][hapmap]
rs3801601	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3801602	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3801603	0.87[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.83[MEX][hapmap];0.96[EUR][1000 genomes]
rs6944512	0.92[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6952700	0.86[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959932	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6965585	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6977169	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6978182	0.90[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7804122	0.93[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][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	nsv607707	chr7:83381032-83646816	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
2	nsv888622	chr7:83526743-83631376	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1020784	chr7:83577402-83687108	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv888623	chr7:83596683-83687622	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv888624	chr7:83596683-83698177	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv888625	chr7:83616528-83687622	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3352967	chr7:83626144-83684599	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3735513	ZNF500	trans	parietal	SCAN
rs3735513	SLC25A40	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:83589000-83654600	Weak transcription	Fetal Stomach	stomach
2	chr7:83591000-83633800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr7:83591200-83634200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr7:83591200-83638400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:83591200-83654600	Weak transcription	Fetal Muscle Leg	muscle
6	chr7:83606000-83654000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr7:83606200-83643200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr7:83609800-83650400	Weak transcription	NHLF	lung
9	chr7:83610200-83642200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr7:83610200-83673000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr7:83622800-83643200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr7:83623600-83634200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr7:83624400-83651600	Weak transcription	Fetal Intestine Small	intestine
14	chr7:83625000-83646800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:83625400-83638200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:83625600-83633800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr7:83625600-83643600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:83626000-83650600	Weak transcription	NH-A	brain
19	chr7:83626400-83638600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:83626600-83636200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr7:83626800-83638800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:83627000-83636600	Weak transcription	Adipose Nuclei	Adipose
23	chr7:83627200-83632000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr7:83627800-83633200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr7:83627800-83633800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr7:83628000-83632600	Weak transcription	Fetal Lung	lung
27	chr7:83628000-83634200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr7:83629400-83632600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr7:83629400-83643600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr7:83629600-83631600	Strong transcription	HUES48 Cell Line	embryonic stem cell
31	chr7:83630200-83633200	Weak transcription	NHDF-Ad	bronchial
32	chr7:83631000-83632200	Enhancers	NHEK	skin
33	chr7:83631000-83632600	Genic enhancers	HUES64 Cell Line	embryonic stem cell
34	chr7:83631200-83632000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr7:83631200-83632000	Enhancers	HMEC	breast
36	chr7:83631200-83632200	Enhancers	Fetal Heart	heart
37	chr7:83631200-83632800	Enhancers	Breast Myoepithelial Primary Cells	Breast

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