Variant report

Variant	rs12237459
Chromosome Location	chr9:94529704-94529705
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10512217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10992087	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10992088	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992089	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10992090	0.83[YRI][hapmap];0.83[AFR][1000 genomes]
rs10992095	0.85[YRI][hapmap];0.81[AFR][1000 genomes]
rs12235606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12235611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12238428	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12685213	0.91[YRI][hapmap];0.83[AFR][1000 genomes]
rs12685849	0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs16907741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907754	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16907761	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16907764	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16907776	0.91[YRI][hapmap]
rs34854279	1.00[ASN][1000 genomes]
rs3802377	0.91[YRI][hapmap]
rs3802378	0.91[YRI][hapmap]
rs3935544	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs4398991	0.85[YRI][hapmap]
rs4452868	1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs4467997	0.85[JPT][hapmap]
rs4595186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4601388	0.83[YRI][hapmap]
rs4744097	0.85[JPT][hapmap]
rs57810120	0.81[AFR][1000 genomes]
rs58210546	0.90[AFR][1000 genomes]
rs60092492	0.81[AFR][1000 genomes]
rs60099576	1.00[ASN][1000 genomes]
rs7026175	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7039620	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs73511086	0.90[AFR][1000 genomes]
rs73511102	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73513203	0.86[AFR][1000 genomes]
rs73651508	0.90[AFR][1000 genomes]
rs7855079	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045332	chr9:94352661-94656016	Active TSS Bivalent Enhancer Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
2	nsv1047426	chr9:94363211-94758114	Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv531631	chr9:94373847-94633213	Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv6612	chr9:94490644-94535738	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1036176	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv540171	chr9:94500213-94639367	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 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	chr9:94477200-94533000	Weak transcription	Fetal Kidney	kidney
2	chr9:94487000-94535400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr9:94519400-94532400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr9:94521200-94532600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:94521200-94532800	Weak transcription	Ovary	ovary
6	chr9:94524400-94533000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr9:94527000-94533000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr9:94527200-94532200	Weak transcription	Fetal Heart	heart
9	chr9:94527200-94533200	Weak transcription	Fetal Intestine Large	intestine
10	chr9:94527600-94538800	Weak transcription	K562	blood
11	chr9:94528000-94530200	Weak transcription	Fetal Intestine Small	intestine
12	chr9:94528400-94529800	Enhancers	Fetal Stomach	stomach
13	chr9:94528600-94533200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr9:94529200-94529800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr9:94529200-94532800	Weak transcription	Fetal Lung	lung
16	chr9:94529400-94529800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr9:94529400-94532200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr9:94529400-94532200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr9:94529400-94539800	Enhancers	Colon Smooth Muscle	Colon

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