Variant report

Variant	rs62389954
Chromosome Location	chr6:12896740-12896741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs13208248	0.88[EUR][1000 genomes]
rs13219256	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332845	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332846	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1332847	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537340	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2876300	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34944538	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35355695	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714951	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4714955	0.80[EUR][1000 genomes]
rs62389955	0.80[EUR][1000 genomes]
rs71562459	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3521000	chr6:12561306-13128519	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	esv3521001	chr6:12561306-13128519	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv830587	chr6:12769661-12939875	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv830588	chr6:12793530-12972493	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:12885600-12908800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:12894000-12908800	Weak transcription	Fetal Brain Female	brain
3	chr6:12894200-12897400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr6:12894200-12897400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr6:12894200-12897400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:12894200-12897600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr6:12894200-12899200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr6:12894200-12903200	Weak transcription	Psoas Muscle	Psoas
9	chr6:12894200-12903400	Weak transcription	HSMM	muscle
10	chr6:12894400-12897400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr6:12894600-12897400	Weak transcription	Fetal Kidney	kidney
12	chr6:12895800-12897000	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr6:12896200-12896800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr6:12896400-12897000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:12896600-12896800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr6:12896600-12896800	Enhancers	Pancreas	Pancrea
17	chr6:12896600-12896800	Bivalent Enhancer	A549	lung
18	chr6:12896600-12904800	Weak transcription	Brain Anterior Caudate	brain
19	chr6:12896600-12911000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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