Variant report

Variant	rs6498256
Chromosome Location	chr16:12049830-12049831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10451099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10468251	0.92[ASN][1000 genomes]
rs10852345	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10852346	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11075035	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11075036	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11075037	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11570137	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11570173	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11864397	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12597378	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12926535	0.86[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12927256	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12928141	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12929036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12929544	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12929852	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12933691	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12934607	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2017662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35965279	0.85[ASN][1000 genomes]
rs365423	0.90[ASN][1000 genomes]
rs366262	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3743591	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851002	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3851003	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs387871	0.91[ASN][1000 genomes]
rs3916675	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57171695	0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58398910	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59320000	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6498255	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6498257	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7189024	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7190636	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7191310	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195514	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs72782778	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8046211	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8047277	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8051343	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs8055129	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8060611	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8062121	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9922422	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9922795	0.87[EUR][1000 genomes];0.91[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	nsv1042660	chr16:11846873-12110435	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv571458	chr16:11925008-12087282	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv482458	chr16:12014925-12145977	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv571459	chr16:12046899-12062396	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12040400-12065400	Weak transcription	Fetal Intestine Small	intestine
2	chr16:12042200-12064400	Weak transcription	Fetal Stomach	stomach
3	chr16:12044800-12052400	Weak transcription	GM12878-XiMat	blood
4	chr16:12044800-12056400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr16:12048600-12064800	Weak transcription	Thymus	Thymus
6	chr16:12049000-12050200	Enhancers	NHLF	lung
7	chr16:12049000-12053400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr16:12049200-12050200	Enhancers	K562	blood
9	chr16:12049200-12050400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr16:12049200-12050800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr16:12049400-12050000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr16:12049400-12050000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr16:12049400-12050200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr16:12049400-12050200	Enhancers	HSMM	muscle
15	chr16:12049600-12050000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr16:12049600-12050000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr16:12049600-12050000	Enhancers	A549	lung
18	chr16:12049600-12050000	Flanking Active TSS	Osteobl	bone
19	chr16:12049600-12050200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr16:12049600-12050200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr16:12049600-12050200	Flanking Active TSS	Hela-S3	cervix
22	chr16:12049600-12050200	Bivalent Enhancer	HepG2	liver
23	chr16:12049600-12050200	Enhancers	HMEC	breast
24	chr16:12049600-12050200	Enhancers	HSMMtube	muscle
25	chr16:12049600-12050200	Flanking Active TSS	NHEK	skin
26	chr16:12049600-12050800	Enhancers	NH-A	brain
27	chr16:12049800-12050000	Enhancers	Muscle Satellite Cultured Cells	--
28	chr16:12049800-12050000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr16:12049800-12050200	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr16:12049800-12050200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr16:12049800-12050200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr16:12049800-12050200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr16:12049800-12050200	Enhancers	Placenta	Placenta
34	chr16:12049800-12050200	Enhancers	HUVEC	blood vessel
35	chr16:12049800-12050200	Flanking Active TSS	NHDF-Ad	bronchial

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