Variant report

Variant	rs62397049
Chromosome Location	chr6:38402197-38402198
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2745385	0.86[ASN][1000 genomes]
rs2814888	0.86[ASN][1000 genomes]
rs4591850	0.87[ASN][1000 genomes]
rs4591851	0.87[ASN][1000 genomes]
rs4598072	0.87[ASN][1000 genomes]
rs4711547	0.87[ASN][1000 genomes]
rs4714160	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4714162	0.93[EUR][1000 genomes]
rs4714163	0.85[ASN][1000 genomes]
rs62397050	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62397055	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6911352	0.85[ASN][1000 genomes]
rs9349081	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9349082	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9357273	0.87[ASN][1000 genomes]
rs9380753	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong 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	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1032358	chr6:38323745-38415855	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1022724	chr6:38332368-38454527	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv602958	chr6:38362024-38446634	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv1030889	chr6:38374812-38450432	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	esv13423	chr6:38391599-38404785	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv2421878	chr6:38391806-38402621	Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv441993	chr6:38391806-38402621	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv514356	chr6:38391934-38402598	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv523561	chr6:38395874-38406736	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38376800-38411400	Weak transcription	Primary T cells from cord blood	blood
2	chr6:38396200-38404400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:38396400-38449800	Weak transcription	Primary B cells from cord blood	blood
4	chr6:38396800-38404600	Weak transcription	NHDF-Ad	bronchial
5	chr6:38398800-38413800	Weak transcription	Aorta	Aorta
6	chr6:38399600-38402400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr6:38400400-38404400	Weak transcription	NH-A	brain
8	chr6:38400400-38410800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr6:38400600-38402600	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr6:38400800-38404400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr6:38400800-38404400	Weak transcription	GM12878-XiMat	blood
12	chr6:38401000-38404200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr6:38401000-38404400	Weak transcription	NHEK	skin
14	chr6:38401600-38402200	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr6:38401600-38402400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr6:38401600-38404400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr6:38401600-38404400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:38401600-38404400	Weak transcription	HMEC	breast
19	chr6:38401800-38402600	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr6:38402000-38402400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links