Variant report

Variant	rs1880679
Chromosome Location	chr10:50767904-50767905
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:50765967..50768022-chr10:50768615..50770437,2	MCF-7	breast:
2	chr10:50749402..50751390-chr10:50767694..50770332,2	K562	blood:
3	chr10:50767252..50769904-chr10:50772463..50774658,3	MCF-7	breast:
4	chr10:50760373..50763303-chr10:50765007..50769387,4	K562	blood:

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1012553	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1012554	0.81[ASN][1000 genomes]
rs10776579	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10776580	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10857503	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10857505	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11101137	0.81[CHB][hapmap]
rs11101153	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11101154	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11527799	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11527805	0.85[CHB][hapmap]
rs11594945	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12161717	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12161719	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12218455	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12218602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12413113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17177703	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17177717	0.86[CHB][hapmap]
rs17784189	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1880680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1917799	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.80[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1917822	0.93[ASN][1000 genomes]
rs2222638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2228524	0.81[ASN][1000 genomes]
rs2228528	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs2281794	0.81[CHB][hapmap]
rs2377901	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2889771	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3750745	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3750748	0.81[CHB][hapmap]
rs3763728	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3793786	0.91[CHB][hapmap];0.98[CHD][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs3793788	0.95[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs4012459	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4253013	0.81[CHB][hapmap]
rs4253024	0.81[ASN][1000 genomes]
rs4253043	0.81[CHB][hapmap]
rs4253060	0.81[CHB][hapmap]
rs4253082	0.95[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.80[ASN][1000 genomes]
rs4253095	0.81[CHB][hapmap]
rs56002988	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57761316	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59219652	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61288726	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7072155	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7100059	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73315045	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7477098	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv831867	chr10:50607857-50788751	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS 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
4	esv3346476	chr10:50610853-50987802	Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv3385048	chr10:50610942-50988537	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50761600-50770400	Weak transcription	HSMM	muscle
2	chr10:50763400-50768400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr10:50763400-50771000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr10:50764400-50768200	Enhancers	Osteobl	bone
5	chr10:50764400-50769200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr10:50766400-50768200	Weak transcription	HMEC	breast
7	chr10:50767000-50770800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr10:50767200-50768600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr10:50767200-50769200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr10:50767200-50769200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr10:50767200-50769200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr10:50767200-50769400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr10:50767400-50768200	Enhancers	HSMMtube	muscle
14	chr10:50767400-50769000	Enhancers	NHDF-Ad	bronchial
15	chr10:50767600-50768000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
16	chr10:50767600-50768000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr10:50767600-50768000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr10:50767600-50768000	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr10:50767600-50768000	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr10:50767600-50768200	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr10:50767600-50768200	Enhancers	Adipose Nuclei	Adipose
22	chr10:50767600-50768400	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr10:50767600-50768400	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr10:50767600-50768600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr10:50767600-50768600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr10:50767600-50768800	Enhancers	Muscle Satellite Cultured Cells	--
27	chr10:50767800-50768200	Enhancers	ES-I3 Cell Line	embryonic stem cell

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