Variant report

Variant	rs10502235
Chromosome Location	chr11:120212423-120212424
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:120205774..120210534-chr11:120211635..120216657,9	MCF-7	breast:
2	chr11:120196112..120199628-chr11:120212006..120215028,3	MCF-7	breast:
3	chr11:120212208..120214300-chr11:120217679..120220181,2	MCF-7	breast:
4	chr11:120210465..120212545-chr11:120324411..120326900,2	K562	blood:
5	chr11:120188995..120191255-chr11:120211216..120212745,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196914	Chromatin interaction
ENSG00000181264	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10750173	0.90[JPT][hapmap]
rs10790381	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10790383	0.90[JPT][hapmap]
rs10892563	0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap]
rs10892565	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10892566	0.90[JPT][hapmap]
rs10892569	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10892575	0.85[EUR][1000 genomes]
rs11217821	0.90[JPT][hapmap]
rs11217843	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11217857	0.87[EUR][1000 genomes]
rs11217874	0.87[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap]
rs11217875	0.81[ASW][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs11601535	0.88[JPT][hapmap]
rs11823264	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11823300	0.94[ASN][1000 genomes]
rs11824032	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11827818	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12270397	0.90[EUR][1000 genomes]
rs12361632	0.98[ASN][1000 genomes]
rs12785387	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12794618	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12806740	0.90[JPT][hapmap]
rs12807097	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17123861	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1812974	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1892894	0.90[JPT][hapmap]
rs1893261	0.90[JPT][hapmap]
rs2276035	1.00[ASW][hapmap];0.88[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs2305008	0.90[JPT][hapmap]
rs2305010	0.90[JPT][hapmap]
rs4381380	0.83[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs4936517	0.89[ASN][1000 genomes]
rs4938799	0.90[JPT][hapmap]
rs4938802	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4938803	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4938804	0.89[JPT][hapmap]
rs4938805	0.90[JPT][hapmap]
rs4938807	0.81[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs4938808	0.90[JPT][hapmap]
rs6589812	0.90[JPT][hapmap]
rs7121779	0.90[JPT][hapmap]
rs7129944	1.00[ASW][hapmap];0.88[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs7131597	0.90[JPT][hapmap]
rs723937	0.89[JPT][hapmap]
rs7933086	0.90[JPT][hapmap]
rs7939137	0.90[JPT][hapmap]
rs7948928	0.90[JPT][hapmap]
rs894839	0.90[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
rs10502235	TMEM136	cis	parietal	SCAN
rs10502235	SIDT2	cis	parietal	SCAN
rs10502235	ARHGEF12	cis	cerebellum	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120208800-120214200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:120208800-120216200	Weak transcription	Esophagus	oesophagus
3	chr11:120208800-120223400	Weak transcription	Gastric	stomach
4	chr11:120209000-120217000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:120209600-120214600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr11:120209600-120215200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:120209600-120216200	Weak transcription	Lung	lung
8	chr11:120209600-120224600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr11:120210400-120214600	Weak transcription	Placenta	Placenta
10	chr11:120210600-120214200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr11:120210600-120214200	Weak transcription	Spleen	Spleen
12	chr11:120210600-120214600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr11:120210600-120214800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr11:120210600-120217000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:120210600-120217000	Weak transcription	Pancreas	Pancrea
16	chr11:120210600-120218200	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:120210800-120213000	Enhancers	Fetal Intestine Large	intestine
18	chr11:120210800-120215000	Weak transcription	Brain Substantia Nigra	brain
19	chr11:120211000-120212600	Enhancers	Brain Anterior Caudate	brain
20	chr11:120211000-120212600	Enhancers	Colon Smooth Muscle	Colon
21	chr11:120211000-120213000	Enhancers	Adipose Nuclei	Adipose
22	chr11:120211000-120213000	Weak transcription	Aorta	Aorta
23	chr11:120211000-120213000	Weak transcription	Brain Angular Gyrus	brain
24	chr11:120211000-120213400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:120211000-120214000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr11:120211000-120214000	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr11:120211000-120214200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
28	chr11:120211000-120214200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr11:120211000-120214200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:120211000-120214200	Weak transcription	Left Ventricle	heart
31	chr11:120211000-120214200	Weak transcription	HSMM	muscle
32	chr11:120211000-120214600	Weak transcription	Fetal Muscle Leg	muscle
33	chr11:120211000-120215000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:120211000-120215000	Weak transcription	Fetal Lung	lung
35	chr11:120211000-120215200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr11:120211000-120215200	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr11:120211000-120217000	Weak transcription	Colonic Mucosa	Colon
38	chr11:120211000-120217000	Weak transcription	Fetal Brain Male	brain
39	chr11:120211000-120217000	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr11:120211000-120217400	Enhancers	Liver	Liver
41	chr11:120211000-120218600	Enhancers	Fetal Heart	heart
42	chr11:120211000-120224400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr11:120211200-120213000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr11:120211200-120213200	Weak transcription	Brain Hippocampus Middle	brain
45	chr11:120211200-120214200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr11:120211200-120214200	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr11:120211200-120218600	Enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr11:120211400-120212800	Flanking Active TSS	K562	blood
49	chr11:120211400-120213400	Enhancers	HepG2	liver
50	chr11:120211400-120214000	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links