Variant report

Variant	rs12066679
Chromosome Location	chr1:57631309-57631310
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11206979	0.85[AFR][1000 genomes]
rs12059674	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs12096519	0.85[AFR][1000 genomes]
rs12164608	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs155308	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6697858	1.00[CEU][hapmap]
rs72917109	1.00[EUR][1000 genomes]
rs72917177	0.83[EUR][1000 genomes]
rs7533282	0.83[YRI][hapmap]
rs7549359	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats 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	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57623200-57635400	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57624000-57644800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:57628000-57632000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:57628000-57632000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:57628200-57631400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:57629000-57632000	Enhancers	iPS-15b Cell Line	embryonic stem cell
7	chr1:57629200-57633200	Weak transcription	Pancreas	Pancrea
8	chr1:57629800-57631400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr1:57630000-57631400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:57630200-57632000	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr1:57630400-57631800	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr1:57630600-57632000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:57630600-57632200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr1:57631000-57631600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:57631000-57632200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr1:57631200-57631800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr1:57631200-57631800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:57631200-57632200	Enhancers	iPS-20b Cell Line	embryonic stem cell

Quick Search:

Input of quick search could be:

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

what's new

Quick links