Variant report

Variant	rs62541922
Chromosome Location	chr9:16870182-16870183
allele	C/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:30)

rs_ID	r²[population]
rs10962638	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10962642	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10962645	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10962647	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10962648	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10962649	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10962652	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10962653	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10962656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10962658	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10962659	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11788047	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11789875	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11792249	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12379687	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62541877	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62541878	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62541879	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62541920	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62541923	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62541926	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62543561	0.83[AFR][1000 genomes]
rs62543578	0.83[AFR][1000 genomes]
rs62543579	0.83[AFR][1000 genomes]
rs62543581	0.83[AFR][1000 genomes]
rs62543582	0.83[AFR][1000 genomes]
rs62543583	0.83[AFR][1000 genomes]
rs62543584	0.83[AFR][1000 genomes]
rs62543585	0.83[AFR][1000 genomes]
rs72713890	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv892652	chr9:16843128-16958312	Bivalent Enhancer Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
4	nsv892653	chr9:16848790-16895610	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
5	nsv1018615	chr9:16865804-16960970	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
6	nsv540074	chr9:16865804-16960970	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:16865000-16872000	Active TSS	Stomach Smooth Muscle	stomach
2	chr9:16866400-16871800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:16866600-16872200	Active TSS	NHLF	lung
4	chr9:16866800-16872000	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr9:16867400-16870200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr9:16867600-16871600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr9:16867600-16872200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr9:16867600-16872200	Active TSS	Colon Smooth Muscle	Colon
9	chr9:16867600-16872400	Active TSS	Ovary	ovary
10	chr9:16867800-16871200	Active TSS	Fetal Stomach	stomach
11	chr9:16868000-16872200	Active TSS	Right Atrium	heart
12	chr9:16868000-16872200	Active TSS	HSMM	muscle
13	chr9:16868200-16872000	Active TSS	HSMMtube	muscle
14	chr9:16868400-16872400	Active TSS	Rectal Smooth Muscle	rectum
15	chr9:16868800-16870600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr9:16868800-16872400	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr9:16869000-16870200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
18	chr9:16869000-16872200	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
19	chr9:16869000-16872400	Active TSS	H1 Cell Line	embryonic stem cell
20	chr9:16869200-16870200	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr9:16869200-16871800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr9:16869200-16872200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr9:16869200-16872200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr9:16869200-16872200	Active TSS	Fetal Intestine Large	intestine
25	chr9:16869400-16870200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
26	chr9:16869400-16870200	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
27	chr9:16869400-16870200	Bivalent/Poised TSS	Left Ventricle	heart
28	chr9:16869400-16870600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
29	chr9:16869400-16870800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
30	chr9:16869400-16871200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr9:16869400-16871200	Flanking Bivalent TSS/Enh	Dnd41	blood
32	chr9:16869400-16871600	Active TSS	Right Ventricle	heart
33	chr9:16869400-16872000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr9:16869400-16872000	Active TSS	Esophagus	oesophagus
35	chr9:16869400-16872000	Active TSS	Lung	lung
36	chr9:16869400-16872200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:16869400-16872200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
38	chr9:16869400-16872400	Active TSS	H9 Cell Line	embryonic stem cell
39	chr9:16869400-16872400	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr9:16869600-16870200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
41	chr9:16869600-16870200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
42	chr9:16869600-16870200	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
43	chr9:16869600-16870200	Flanking Active TSS	HUVEC	blood vessel
44	chr9:16869600-16870400	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
45	chr9:16869600-16870400	Bivalent/Poised TSS	Brain Angular Gyrus	brain
46	chr9:16869600-16871000	Bivalent Enhancer	Fetal Heart	heart
47	chr9:16869600-16871200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr9:16869600-16871600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr9:16869600-16871800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr9:16869600-16872000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links