Variant report

Variant	rs2725200
Chromosome Location	chr10:50374171-50374172
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:50374066..50375952-chr10:50506772..50508302,2	K562	blood:
2	chr10:50372843..50375654-chr10:50384413..50387038,2	MCF-7	breast:
3	chr10:50372128..50374290-chr10:50587690..50589612,2	K562	blood:

Variant related genes	Relation type
ENSG00000204161	Chromatin interaction
ENSG00000236208	Chromatin interaction
ENSG00000177354	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10218995	0.83[JPT][hapmap]
rs11100988	1.00[JPT][hapmap]
rs12255055	0.81[CHB][hapmap]
rs17175928	0.83[MEX][hapmap]
rs2002436	0.86[ASN][1000 genomes]
rs2002728	0.83[JPT][hapmap]
rs2003044	0.88[CHB][hapmap];0.84[CHD][hapmap]
rs2377953	0.81[ASN][1000 genomes]
rs2466748	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2466756	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2725179	0.82[CHB][hapmap]
rs2725180	0.83[JPT][hapmap]
rs2725181	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs2725192	0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2725193	0.81[ASN][1000 genomes]
rs2725194	0.83[ASN][1000 genomes]
rs2804928	0.82[ASN][1000 genomes]
rs2804930	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2804931	0.88[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.94[MEX][hapmap];0.80[AMR][1000 genomes]
rs2804932	0.88[CHB][hapmap];0.89[CHD][hapmap];0.94[MEX][hapmap]
rs2804933	0.87[JPT][hapmap]
rs2804934	0.82[CHB][hapmap];0.84[CHD][hapmap]
rs2804936	0.83[JPT][hapmap]
rs4073712	1.00[JPT][hapmap]
rs4298825	0.88[MEX][hapmap]
rs4319434	0.83[JPT][hapmap]
rs4319435	0.82[JPT][hapmap]
rs4344406	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4417190	1.00[JPT][hapmap]
rs4488117	0.88[MEX][hapmap]
rs4558091	1.00[JPT][hapmap]
rs4620641	1.00[JPT][hapmap]
rs4838446	1.00[JPT][hapmap]
rs4838447	1.00[JPT][hapmap]
rs6537499	0.83[JPT][hapmap]
rs7072243	1.00[JPT][hapmap]
rs7073645	0.83[JPT][hapmap]
rs7094217	0.83[JPT][hapmap]
rs9418839	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS 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 lncRNA	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2725200	WDFY4	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50359000-50382200	Weak transcription	Left Ventricle	heart
2	chr10:50359200-50375400	Weak transcription	Right Atrium	heart
3	chr10:50362400-50380600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr10:50365400-50374800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr10:50365400-50374800	Weak transcription	Lung	lung
6	chr10:50366200-50378200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr10:50366800-50375400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr10:50367600-50376200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr10:50367600-50384600	Weak transcription	Dnd41	blood
10	chr10:50368000-50375600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr10:50368200-50380800	Weak transcription	Esophagus	oesophagus
12	chr10:50369000-50377200	Weak transcription	Brain Angular Gyrus	brain
13	chr10:50369600-50380400	Weak transcription	Gastric	stomach
14	chr10:50370000-50375000	Weak transcription	Brain Substantia Nigra	brain
15	chr10:50371600-50377200	Weak transcription	Primary B cells from cord blood	blood
16	chr10:50372000-50384000	Weak transcription	Colonic Mucosa	Colon
17	chr10:50372400-50377000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr10:50372400-50377000	Weak transcription	NHDF-Ad	bronchial
19	chr10:50372800-50374200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr10:50372800-50375600	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr10:50372800-50376800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr10:50372800-50377600	Weak transcription	Brain Hippocampus Middle	brain
23	chr10:50372800-50386200	Weak transcription	Pancreas	Pancrea
24	chr10:50373000-50375200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr10:50373000-50376800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr10:50373200-50375000	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr10:50373200-50375600	Strong transcription	Adipose Nuclei	Adipose
28	chr10:50373200-50376400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr10:50373200-50376400	Strong transcription	Duodenum Mucosa	Duodenum
30	chr10:50373200-50385200	Weak transcription	Colon Smooth Muscle	Colon
31	chr10:50373400-50374800	Strong transcription	Right Ventricle	heart
32	chr10:50373400-50376000	Strong transcription	Spleen	Spleen
33	chr10:50373600-50374200	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr10:50373600-50374800	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr10:50373600-50383000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr10:50373800-50374200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr10:50373800-50374800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr10:50374000-50374400	Weak transcription	Fetal Muscle Leg	muscle
39	chr10:50374000-50374800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr10:50374000-50375200	Strong transcription	Skeletal Muscle Male	skeletal muscle
41	chr10:50374000-50375200	Flanking Active TSS	K562	blood
42	chr10:50374000-50375600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links