Variant report

Variant	rs12090414
Chromosome Location	chr1:57600403-57600404
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11206975	1.00[JPT][hapmap]
rs12408256	1.00[JPT][hapmap]
rs12564278	1.00[JPT][hapmap]
rs12566320	1.00[JPT][hapmap]
rs17115105	1.00[JPT][hapmap]
rs17115108	1.00[JPT][hapmap]
rs17115146	1.00[JPT][hapmap]
rs17115155	1.00[JPT][hapmap]
rs476568	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs484064	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs490793	0.89[CEU][hapmap];0.88[EUR][1000 genomes]
rs502701	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs506832	0.86[EUR][1000 genomes]
rs510824	0.89[CEU][hapmap];0.81[GIH][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes]
rs513259	0.89[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs519401	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs535415	1.00[ASW][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs537307	0.89[CEU][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs546020	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs549622	0.94[CEU][hapmap];0.83[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs550511	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs553453	1.00[ASW][hapmap];0.89[CEU][hapmap];0.81[GIH][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs553508	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs556204	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs561258	0.94[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563921	0.94[CEU][hapmap];0.83[GIH][hapmap];0.90[TSI][hapmap];0.86[EUR][1000 genomes]
rs564665	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs578962	0.90[EUR][1000 genomes]
rs579057	0.88[CEU][hapmap];0.90[EUR][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	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	nsv428752	chr1:57455083-57605082	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	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
4	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:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57551400-57622000	Weak transcription	Fetal Intestine Small	intestine
2	chr1:57589400-57608600	Weak transcription	Fetal Intestine Large	intestine
3	chr1:57590600-57601400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:57595400-57600800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:57595600-57604200	Weak transcription	Liver	Liver
6	chr1:57596600-57601000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:57596800-57601200	Enhancers	NHEK	skin
8	chr1:57597000-57600600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:57599400-57604000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:57600200-57601200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:57600400-57600600	Enhancers	HMEC	breast

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