Variant report

Variant	rs7252585
Chromosome Location	chr19:21657943-21657944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10420016	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1114305	0.81[CHB][hapmap]
rs12974758	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12975081	0.85[JPT][hapmap]
rs13346641	0.86[CEU][hapmap]
rs1781867	0.95[CEU][hapmap]
rs1781872	0.95[CEU][hapmap]
rs1781873	0.81[JPT][hapmap]
rs1879234	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1967182	0.91[CEU][hapmap]
rs2012013	0.81[JPT][hapmap]
rs2086319	0.81[JPT][hapmap]
rs2088762	0.81[JPT][hapmap]
rs2173727	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2359144	0.90[CEU][hapmap]
rs2359155	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2562398	0.83[EUR][1000 genomes]
rs2562402	0.80[CHB][hapmap]
rs2562408	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2562417	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2562428	0.82[ASN][1000 genomes]
rs2562435	0.85[JPT][hapmap]
rs2562456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2562466	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2562468	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2562471	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2562474	0.81[ASN][1000 genomes]
rs2562487	0.85[ASN][1000 genomes]
rs2562507	0.83[EUR][1000 genomes]
rs2562508	0.83[EUR][1000 genomes]
rs2650773	0.83[ASN][1000 genomes]
rs2650784	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2650792	0.83[EUR][1000 genomes]
rs2650793	0.90[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650798	0.81[JPT][hapmap]
rs2650801	0.82[ASN][1000 genomes]
rs2650804	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650805	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650814	0.83[ASN][1000 genomes]
rs2650819	0.83[ASN][1000 genomes]
rs2650825	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2650844	0.90[CEU][hapmap]
rs2681377	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2681388	0.83[EUR][1000 genomes]
rs2681389	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2681392	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2914626	0.81[CHB][hapmap]
rs2914638	0.81[JPT][hapmap]
rs2914645	0.81[JPT][hapmap]
rs2914646	0.83[ASN][1000 genomes]
rs2937174	0.81[JPT][hapmap]
rs2946790	0.83[EUR][1000 genomes]
rs2968045	0.81[JPT][hapmap]
rs2968046	0.80[CHB][hapmap]
rs2968076	0.85[ASN][1000 genomes]
rs2968078	0.83[ASN][1000 genomes]
rs2968082	0.81[CHB][hapmap]
rs35008138	0.83[EUR][1000 genomes]
rs4315457	0.81[JPT][hapmap]
rs4321312	0.95[CEU][hapmap]
rs4359573	0.95[CEU][hapmap]
rs4524067	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4638726	0.91[CEU][hapmap]
rs472472	0.80[JPT][hapmap]
rs4809145	0.93[CHB][hapmap]
rs499445	0.80[JPT][hapmap]
rs541639	0.80[JPT][hapmap]
rs62110163	0.83[EUR][1000 genomes]
rs627522	0.95[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs6511250	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6511253	0.95[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6511254	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6511256	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6511258	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7247411	0.81[JPT][hapmap]
rs7252261	0.81[JPT][hapmap]
rs7257857	0.81[JPT][hapmap]
rs7260065	0.90[CEU][hapmap]
rs8103325	0.81[JPT][hapmap]
rs8106025	0.83[ASN][1000 genomes]
rs8112775	0.80[JPT][hapmap]
rs924485	0.81[JPT][hapmap]
rs9304986	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9304987	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3518033	chr19:21278465-21747567	Strong transcription Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3518034	chr19:21278465-21747567	ZNF genes & repeats Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	esv2751783	chr19:21465822-21726337	Strong transcription ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	esv3363678	chr19:21483148-21756908	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	nsv961284	chr19:21636687-21659271	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7252585	RP11-678G14.3	cis	Adipose Subcutaneous	GTEx
rs7252585	ZNF708	cis	Muscle Skeletal	GTEx
rs7252585	ZNF708	cis	Skin Sun Exposed Lower leg	GTEx
rs7252585	CTD-2561J22.5	cis	Thyroid	GTEx
rs7252585	RP11-678G14.2	cis	Adipose Subcutaneous	GTEx
rs7252585	ZNF708	cis	lung	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21657000-21658000	Active TSS	Colon Smooth Muscle	Colon
2	chr19:21657000-21658200	Active TSS	Brain Inferior Temporal Lobe	brain
3	chr19:21657000-21658400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr19:21657000-21658600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:21657000-21659000	Active TSS	iPS-15b Cell Line	embryonic stem cell
6	chr19:21657200-21658000	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
7	chr19:21657200-21658200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr19:21657200-21658200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:21657200-21658200	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr19:21657200-21658200	Flanking Active TSS	Brain Hippocampus Middle	brain
11	chr19:21657200-21658200	Active TSS	Brain Substantia Nigra	brain
12	chr19:21657200-21658200	Active TSS	Fetal Kidney	kidney
13	chr19:21657200-21658200	Active TSS	Right Atrium	heart
14	chr19:21657200-21658200	Active TSS	Right Ventricle	heart
15	chr19:21657200-21658400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr19:21657200-21658400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr19:21657200-21658400	Active TSS	Brain Angular Gyrus	brain
18	chr19:21657200-21658400	Active TSS	Fetal Intestine Small	intestine
19	chr19:21657200-21658600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:21657200-21658800	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr19:21657200-21658800	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr19:21657200-21659000	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr19:21657200-21659200	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr19:21657400-21658000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
25	chr19:21657400-21658000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:21657400-21658000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:21657400-21658000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr19:21657400-21658000	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
29	chr19:21657400-21658000	Active TSS	Cortex derived primary cultured neurospheres	brain
30	chr19:21657400-21658000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr19:21657400-21658000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:21657400-21658000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr19:21657400-21658000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
34	chr19:21657400-21658000	Active TSS	Aorta	Aorta
35	chr19:21657400-21658000	ZNF genes & repeats	Liver	Liver
36	chr19:21657400-21658000	ZNF genes & repeats	Esophagus	oesophagus
37	chr19:21657400-21658000	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr19:21657400-21658000	Flanking Active TSS	Fetal Muscle Leg	muscle
39	chr19:21657400-21658000	ZNF genes & repeats	Lung	lung
40	chr19:21657400-21658000	Active TSS	Rectal Mucosa Donor 31	rectum
41	chr19:21657400-21658000	Bivalent/Poised TSS	Skeletal Muscle Male	skeletal muscle
42	chr19:21657400-21658000	Active TSS	Stomach Mucosa	stomach
43	chr19:21657400-21658000	Active TSS	NHDF-Ad	bronchial
44	chr19:21657400-21658200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr19:21657400-21658200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:21657400-21658200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr19:21657400-21658200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
48	chr19:21657400-21658200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
49	chr19:21657400-21658200	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr19:21657400-21658200	Active TSS	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links