Variant report

Variant	rs503473
Chromosome Location	chr11:120355230-120355231
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:120355108..120357565-chr11:120365015..120366916,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10750173	0.81[JPT][hapmap]
rs10790379	0.84[EUR][1000 genomes]
rs10790383	0.81[JPT][hapmap]
rs10892566	0.81[JPT][hapmap]
rs10892568	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11217816	0.85[JPT][hapmap]
rs11217821	0.81[JPT][hapmap]
rs11601535	0.83[JPT][hapmap]
rs12806740	0.81[JPT][hapmap]
rs1892894	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs1893261	0.81[JPT][hapmap]
rs2305008	0.81[JPT][hapmap]
rs2305010	0.81[JPT][hapmap]
rs3809059	0.92[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap]
rs4245212	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4938799	0.81[JPT][hapmap]
rs4938804	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs4938805	0.81[JPT][hapmap]
rs4938808	0.81[JPT][hapmap]
rs496034	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs496248	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs538661	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs632137	0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6589812	0.80[CHD][hapmap];0.81[JPT][hapmap]
rs661139	0.83[ASN][1000 genomes]
rs7116481	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7121779	0.81[JPT][hapmap]
rs7131597	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs723937	0.81[JPT][hapmap]
rs7933086	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs7939137	0.81[CHD][hapmap];0.81[JPT][hapmap]
rs7940963	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7948928	0.81[JPT][hapmap]
rs894839	0.81[JPT][hapmap]

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	nsv1054057	chr11:119781953-120519770	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv541178	chr11:119781953-120519770	Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv529003	chr11:120209386-120355230	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs503473	TMEM136	cis	parietal	SCAN
rs503473	ARHGEF12	cis	parietal	SCAN
rs503473	ARHGEF12	cis	cerebellum	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120303600-120355600	Weak transcription	Stomach Mucosa	stomach
2	chr11:120304800-120359400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr11:120308000-120359000	Strong transcription	Placenta	Placenta
4	chr11:120308400-120357800	Strong transcription	Adipose Nuclei	Adipose
5	chr11:120310400-120358000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr11:120311200-120357200	Strong transcription	Duodenum Smooth Muscle	Duodenum
7	chr11:120312800-120357800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr11:120314200-120362200	Strong transcription	Liver	Liver
9	chr11:120316400-120382000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:120320000-120358000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:120320200-120357600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:120321000-120358000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:120329000-120358800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr11:120335200-120359600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr11:120336200-120358600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr11:120337600-120357200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:120339800-120362200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr11:120341400-120355600	Weak transcription	Psoas Muscle	Psoas
19	chr11:120342200-120358400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:120342800-120358800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:120343600-120357200	Strong transcription	Stomach Smooth Muscle	stomach
22	chr11:120343800-120358000	Strong transcription	Osteobl	bone
23	chr11:120344000-120359200	Strong transcription	Rectal Mucosa Donor 31	rectum
24	chr11:120344200-120358600	Strong transcription	Brain Inferior Temporal Lobe	brain
25	chr11:120345200-120358400	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr11:120345400-120356600	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:120345600-120357400	Strong transcription	Fetal Muscle Leg	muscle
28	chr11:120346400-120359800	Weak transcription	Primary B cells from cord blood	blood
29	chr11:120346800-120357400	Strong transcription	Fetal Stomach	stomach
30	chr11:120348800-120357200	Strong transcription	Brain Germinal Matrix	brain
31	chr11:120350400-120356400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr11:120350400-120358800	Strong transcription	Fetal Muscle Trunk	muscle
33	chr11:120352200-120355400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:120352200-120355400	Weak transcription	Spleen	Spleen
35	chr11:120352200-120355400	Weak transcription	NHLF	lung
36	chr11:120352200-120355600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr11:120352200-120356400	Weak transcription	Right Atrium	heart
38	chr11:120352400-120355400	Weak transcription	Colonic Mucosa	Colon
39	chr11:120352400-120355400	Weak transcription	Gastric	stomach
40	chr11:120352400-120358600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:120352600-120355400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr11:120352600-120355400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr11:120352600-120355400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr11:120352600-120357400	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr11:120353000-120355400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr11:120353000-120355400	Weak transcription	Brain Cingulate Gyrus	brain
47	chr11:120353000-120355400	Weak transcription	Ovary	ovary
48	chr11:120353000-120355400	Weak transcription	HUVEC	blood vessel
49	chr11:120353000-120355400	Weak transcription	K562	blood
50	chr11:120353000-120359800	Weak transcription	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links