Variant report

Variant	rs10256256
Chromosome Location	chr7:48081581-48081582
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	chr7:48080536..48082874-chr7:48084498..48087203,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10225968	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs10247913	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10253220	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10253238	0.84[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10261930	0.90[JPT][hapmap];0.91[EUR][1000 genomes]
rs10951937	0.89[JPT][hapmap];0.85[EUR][1000 genomes]
rs10951938	0.87[CEU][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs10951940	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10951941	0.92[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10951942	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11761275	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11762077	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11764799	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11766144	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11766891	0.95[EUR][1000 genomes]
rs11767002	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11768277	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11772387	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11772633	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11773348	0.84[EUR][1000 genomes]
rs12535580	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12537979	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12702405	0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12702406	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1318327	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13230023	0.84[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs1574242	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1915960	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs1915962	0.92[CEU][hapmap];0.90[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1915965	0.89[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs1915966	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1915967	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1915968	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1915971	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1915972	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2037482	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2140113	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs2348666	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2348667	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2348669	0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2348670	0.85[EUR][1000 genomes]
rs2686783	0.80[EUR][1000 genomes]
rs2708851	0.85[TSI][hapmap];0.81[EUR][1000 genomes]
rs2708883	0.82[TSI][hapmap]
rs2708909	0.85[TSI][hapmap]
rs2881991	0.88[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2881992	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4332046	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4354227	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4618593	0.89[CEU][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes]
rs6978838	1.00[CEU][hapmap];0.80[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6979699	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7357251	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7357327	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7456745	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7779252	0.84[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7791084	0.88[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7791572	0.88[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7791823	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7807611	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7807612	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7807654	0.88[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7807750	0.88[CEU][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7808462	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9690905	0.92[CEU][hapmap];0.90[JPT][hapmap];0.95[EUR][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	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv888004	chr7:48028771-48120717	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10256256	PKD1L1	cis	cerebellum	SCAN
rs10256256	C7orf57	cis	Esophagus Mucosa	GTEx
rs10256256	ABCA13	cis	parietal	SCAN
rs10256256	UPP1	cis	cerebellum	SCAN
rs10256256	UPP1	cis	Muscle Skeletal	GTEx
rs10256256	PKD1L1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48078600-48083200	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr7:48078800-48081600	Enhancers	H1 Cell Line	embryonic stem cell
3	chr7:48078800-48083000	Enhancers	HUES6 Cell Line	embryonic stem cell
4	chr7:48079200-48081800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr7:48079600-48082800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr7:48079600-48083000	Enhancers	HMEC	breast
7	chr7:48079600-48083200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr7:48079800-48083000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:48080000-48082000	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr7:48080000-48082600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr7:48080200-48082000	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr7:48080400-48081600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:48080600-48081800	Enhancers	NHDF-Ad	bronchial
14	chr7:48080600-48082000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr7:48080600-48082000	Enhancers	HSMM	muscle
16	chr7:48080600-48082200	Enhancers	Muscle Satellite Cultured Cells	--
17	chr7:48080600-48082200	Enhancers	Osteobl	bone
18	chr7:48080600-48082800	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr7:48080800-48081800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr7:48080800-48082000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr7:48080800-48082200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:48080800-48082200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr7:48080800-48082600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr7:48080800-48082600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
25	chr7:48080800-48082600	Enhancers	NH-A	brain
26	chr7:48080800-48082800	Enhancers	HUVEC	blood vessel
27	chr7:48080800-48091600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr7:48081000-48082000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr7:48081000-48082200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr7:48081000-48082400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr7:48081000-48082600	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr7:48081200-48081600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr7:48081200-48082400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr7:48081200-48082400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr7:48081200-48082600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:48081200-48087800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr7:48081400-48081800	Flanking Active TSS	NHEK	skin
38	chr7:48081400-48082000	Enhancers	Hela-S3	cervix
39	chr7:48081400-48083000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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