Variant report

Variant	rs11202600
Chromosome Location	chr10:89682833-89682834
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr10:89682826-89683280	GM12878	blood:	n/a	n/a
2	POLR2A	chr10:89682810-89683358	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr10:89679106..89681199-chr10:89681260..89684202,3	K562	blood:
2	chr10:89673644..89678140-chr10:89679296..89683460,5	K562	blood:
3	chr10:89620410..89622010-chr10:89680788..89683163,3	MCF-7	breast:

Variant related genes	Relation type
PTEN	TF binding region

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1022427	1.00[CEU][hapmap]
rs10430712	0.84[EUR][1000 genomes]
rs10430715	1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10509533	0.86[JPT][hapmap];1.00[MEX][hapmap];0.82[TSI][hapmap]
rs11202595	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11202597	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11202599	0.91[ASN][1000 genomes]
rs11202607	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11202612	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11202613	0.87[EUR][1000 genomes]
rs11202616	0.87[EUR][1000 genomes]
rs11202617	0.87[EUR][1000 genomes]
rs11202618	0.87[EUR][1000 genomes]
rs11202619	0.87[EUR][1000 genomes]
rs11202620	0.87[EUR][1000 genomes]
rs11202621	0.87[EUR][1000 genomes]
rs11202623	0.86[EUR][1000 genomes]
rs11202625	0.87[EUR][1000 genomes]
rs11202626	0.87[EUR][1000 genomes]
rs11202629	0.86[EUR][1000 genomes]
rs11525294	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12218012	0.86[EUR][1000 genomes]
rs12220739	0.93[ASN][1000 genomes]
rs1234218	1.00[CEU][hapmap]
rs1234219	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1234220	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[ASN][1000 genomes]
rs1234223	1.00[CHB][hapmap];0.94[CHD][hapmap];0.84[ASN][1000 genomes]
rs34366180	0.89[ASN][1000 genomes]
rs35755883	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1793518	chr10:89625582-89733420	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	esv1798260	chr10:89625582-89733420	Weak transcription Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1044043	chr10:89678935-89701069	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11202600	FCER2	trans	brain	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89647000-89711200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr10:89648000-89683000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr10:89663600-89686400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr10:89663600-89687400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr10:89663800-89725400	Weak transcription	Colonic Mucosa	Colon
6	chr10:89666000-89712400	Weak transcription	Fetal Brain Male	brain
7	chr10:89673600-89726000	Weak transcription	Brain Substantia Nigra	brain
8	chr10:89674000-89685600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr10:89674200-89695200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr10:89674200-89711000	Weak transcription	HepG2	liver
11	chr10:89674600-89684400	Weak transcription	Fetal Kidney	kidney
12	chr10:89674600-89686400	Weak transcription	HSMMtube	muscle
13	chr10:89674600-89687000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr10:89674600-89689800	Weak transcription	Fetal Lung	lung
15	chr10:89674600-89695600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr10:89674800-89724400	Weak transcription	Fetal Brain Female	brain
17	chr10:89675400-89686400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr10:89675400-89726000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr10:89675600-89683800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr10:89675600-89685400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr10:89675600-89686200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr10:89675600-89687200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr10:89675600-89705000	Weak transcription	Fetal Stomach	stomach
24	chr10:89675600-89705200	Weak transcription	Esophagus	oesophagus
25	chr10:89676200-89683000	Weak transcription	Fetal Intestine Large	intestine
26	chr10:89676200-89686400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr10:89676600-89683800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr10:89676600-89683800	Weak transcription	NHDF-Ad	bronchial
29	chr10:89676600-89685400	Weak transcription	NH-A	brain
30	chr10:89676600-89685400	Weak transcription	Osteobl	bone
31	chr10:89676600-89685600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr10:89676600-89686200	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr10:89676600-89686400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr10:89676600-89686400	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr10:89676600-89686400	Weak transcription	HMEC	breast
36	chr10:89676600-89686600	Weak transcription	Small Intestine	intestine
37	chr10:89676600-89695400	Weak transcription	Brain Anterior Caudate	brain
38	chr10:89676800-89685400	Weak transcription	K562	blood
39	chr10:89676800-89686400	Weak transcription	NHEK	skin
40	chr10:89676800-89691000	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr10:89677000-89686400	Weak transcription	NHLF	lung
42	chr10:89677200-89688200	Weak transcription	A549	lung
43	chr10:89678000-89683800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr10:89678000-89694200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr10:89678200-89683800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr10:89678600-89683800	Weak transcription	Stomach Mucosa	stomach
47	chr10:89678600-89686400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr10:89678800-89683000	Weak transcription	Duodenum Smooth Muscle	Duodenum
49	chr10:89678800-89687000	Weak transcription	Liver	Liver
50	chr10:89679800-89684000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links