Variant report

Variant	rs10810580
Chromosome Location	chr9:16629923-16629924
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1003069	0.96[CEU][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1003070	0.93[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10810579	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs10810581	0.88[ASW][hapmap];0.92[CEU][hapmap];0.87[LWK][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs10962519	0.86[YRI][hapmap]
rs10962520	0.83[YRI][hapmap]
rs13290470	0.82[CEU][hapmap]
rs1337387	0.81[CEU][hapmap]
rs2275256	0.83[YRI][hapmap]
rs4131372	0.81[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs4961728	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7019299	0.83[YRI][hapmap];0.81[AMR][1000 genomes]
rs7033512	0.81[AMR][1000 genomes]
rs7034582	0.83[AFR][1000 genomes]
rs7043298	0.83[YRI][hapmap]
rs958557	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530933	chr9:16251206-16830845	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv530934	chr9:16281246-16779432	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv1032856	chr9:16465330-16773471	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv540073	chr9:16465330-16773471	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv430000	chr9:16603483-16671045	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10810580	SLC24A2	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16624200-16630400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr9:16625000-16630000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:16627000-16636600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:16627200-16631800	Weak transcription	NHEK	skin
5	chr9:16627200-16637000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr9:16628800-16630200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr9:16628800-16630600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr9:16629000-16635200	Weak transcription	Fetal Lung	lung
9	chr9:16629000-16640600	Weak transcription	HSMMtube	muscle
10	chr9:16629200-16630000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr9:16629200-16637200	Weak transcription	Fetal Stomach	stomach
12	chr9:16629200-16642200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr9:16629400-16630200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:16629400-16640400	Weak transcription	HSMM	muscle
15	chr9:16629600-16630000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr9:16629600-16630200	Enhancers	Colon Smooth Muscle	Colon
17	chr9:16629600-16634000	Weak transcription	NHLF	lung
18	chr9:16629600-16635800	Weak transcription	Ovary	ovary
19	chr9:16629600-16635800	Weak transcription	NHDF-Ad	bronchial
20	chr9:16629600-16637400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:16629600-16638000	Weak transcription	Osteobl	bone
22	chr9:16629600-16653600	Weak transcription	HUVEC	blood vessel
23	chr9:16629800-16630200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr9:16629800-16630200	Enhancers	Rectal Smooth Muscle	rectum

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