Variant report

Variant	rs10962559
Chromosome Location	chr9:16743408-16743409
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10481558	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10756788	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10756789	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10756790	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10756796	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10756798	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10756800	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10756801	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10810598	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10810601	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10810604	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10810606	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10810607	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10810611	0.86[EUR][1000 genomes]
rs10962548	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10962554	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10962560	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11787694	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs13284478	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13290007	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs13296274	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1330303	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1952689	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34259118	0.84[AMR][1000 genomes]
rs35007358	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62541515	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9987471	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1024799	chr9:16631890-17431827	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	esv2758627	chr9:16641966-16809203	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	esv2759673	chr9:16641966-16809203	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription 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	10 gene(s)	inside rSNPs	diseases
8	nsv892649	chr9:16677221-16761597	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv892650	chr9:16696187-16950860	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16728200-16744600	Weak transcription	Fetal Intestine Large	intestine
2	chr9:16728400-16744200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr9:16729400-16744400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr9:16729600-16744200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr9:16730000-16744600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr9:16730200-16748200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr9:16730600-16744400	Weak transcription	Colon Smooth Muscle	Colon
8	chr9:16731200-16744600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr9:16733400-16743800	Weak transcription	HSMM	muscle
10	chr9:16733800-16749200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:16734800-16745000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:16735000-16743600	Weak transcription	NHLF	lung
13	chr9:16735000-16749200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr9:16735200-16744400	Weak transcription	Fetal Lung	lung
15	chr9:16736200-16744600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr9:16738600-16745200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr9:16738600-16749200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr9:16739200-16745200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr9:16739200-16745400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr9:16740200-16744400	Weak transcription	Ovary	ovary
21	chr9:16742600-16743600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:16742600-16746000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr9:16743200-16743800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr9:16743200-16743800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr9:16743200-16745600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:16743400-16743600	Enhancers	Osteobl	bone
27	chr9:16743400-16743800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr9:16743400-16744000	Enhancers	Fetal Stomach	stomach
29	chr9:16743400-16745600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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