Variant report

Variant	rs6872282
Chromosome Location	chr5:40704090-40704091
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1002424	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10036575	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10038769	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10042750	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10055925	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10071679	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs10074991	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10078575	0.99[ASN][1000 genomes]
rs13361707	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1345778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1692252	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2329353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs28540420	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3805497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4509070	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4957342	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57806386	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60770691	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6860328	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6868517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap]
rs6873054	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6897169	0.97[ASN][1000 genomes]
rs7705504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap]
rs7716285	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7726270	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7730368	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs980093	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880539	chr5:40662257-40713645	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
2	esv3432300	chr5:40698244-40726882	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40688800-40718600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:40692400-40741200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr5:40692800-40721000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:40692800-40733800	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr5:40692800-40735000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:40693600-40727400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:40694800-40721000	Weak transcription	Thymus	Thymus
8	chr5:40695200-40715800	Weak transcription	Primary B cells from cord blood	blood
9	chr5:40695200-40727000	Weak transcription	HSMM	muscle
10	chr5:40699000-40720800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr5:40700400-40706800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr5:40700800-40712800	Weak transcription	Gastric	stomach
13	chr5:40700800-40720600	Weak transcription	Left Ventricle	heart
14	chr5:40700800-40720800	Weak transcription	Spleen	Spleen
15	chr5:40700800-40722200	Weak transcription	Lung	lung
16	chr5:40701000-40720800	Weak transcription	Aorta	Aorta
17	chr5:40701000-40722200	Weak transcription	Esophagus	oesophagus
18	chr5:40701400-40711400	Weak transcription	Fetal Intestine Large	intestine
19	chr5:40702400-40705200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:40702400-40715800	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr5:40702600-40706000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr5:40702600-40706000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr5:40702600-40711800	Weak transcription	Fetal Kidney	kidney
24	chr5:40702800-40705800	Weak transcription	Primary T cells from cord blood	blood
25	chr5:40702800-40715200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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