Variant report

Variant	rs11217875
Chromosome Location	chr11:120325559-120325560
allele	A/C
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	chr11:120324260-120328029	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:120322636..120325614-chr11:120329269..120331112,2	K562	blood:
2	chr11:120210465..120212545-chr11:120324411..120326900,2	K562	blood:

Variant related genes	Relation type
ARHGEF12	TF binding region
ENSG00000269601	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10502235	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]
rs10750173	0.89[JPT][hapmap]
rs10790381	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10790383	0.89[JPT][hapmap]
rs10892563	0.82[CHB][hapmap];0.80[CHD][hapmap];0.94[JPT][hapmap]
rs10892565	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10892566	0.89[JPT][hapmap]
rs10892569	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10892575	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11217821	0.89[JPT][hapmap]
rs11217843	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11217857	0.80[AFR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11217866	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11217874	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11217878	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11217887	0.83[ASN][1000 genomes]
rs11601535	0.88[JPT][hapmap]
rs11823264	0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11824032	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11827818	0.81[ASW][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap]
rs12270397	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12794618	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12806740	0.89[JPT][hapmap]
rs12807097	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17123861	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1892894	0.89[JPT][hapmap]
rs1893261	0.89[JPT][hapmap]
rs2276035	0.81[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2305008	0.89[JPT][hapmap]
rs2305010	0.89[JPT][hapmap]
rs4381380	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4936518	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4938799	0.89[JPT][hapmap]
rs4938802	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4938803	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4938804	0.89[JPT][hapmap]
rs4938805	0.81[CHD][hapmap];0.89[JPT][hapmap]
rs4938806	0.92[ASN][1000 genomes]
rs4938807	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4938808	0.89[JPT][hapmap]
rs56693116	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6589810	0.92[ASN][1000 genomes]
rs6589812	0.89[JPT][hapmap]
rs6589813	0.94[ASN][1000 genomes]
rs7101415	0.92[ASN][1000 genomes]
rs7107211	0.82[ASN][1000 genomes]
rs7115714	0.93[ASN][1000 genomes]
rs7121779	0.89[JPT][hapmap]
rs7129944	0.81[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7131597	0.89[JPT][hapmap]
rs71484170	0.82[AMR][1000 genomes]
rs723937	0.89[JPT][hapmap]
rs7924772	0.88[ASN][1000 genomes]
rs7933086	0.89[JPT][hapmap]
rs7939137	0.89[JPT][hapmap]
rs7948928	0.89[JPT][hapmap]
rs894839	0.89[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
rs11217875	TMEM136	cis	parietal	SCAN
rs11217875	SIDT2	cis	parietal	SCAN
rs11217875	ARHGEF12	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:120301400-120355200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:120303600-120355600	Weak transcription	Stomach Mucosa	stomach
3	chr11:120303800-120328000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr11:120304600-120329800	Strong transcription	HSMM	muscle
5	chr11:120304800-120359400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr11:120306600-120341200	Strong transcription	Osteobl	bone
7	chr11:120306800-120341600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr11:120307000-120335800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr11:120307000-120341200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:120307600-120334600	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr11:120308000-120341800	Strong transcription	Fetal Intestine Large	intestine
12	chr11:120308000-120352600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr11:120308000-120359000	Strong transcription	Placenta	Placenta
14	chr11:120308200-120330600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr11:120308200-120336400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr11:120308400-120333200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr11:120308400-120334600	Strong transcription	Rectal Mucosa Donor 31	rectum
18	chr11:120308400-120339000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
19	chr11:120308400-120339000	Strong transcription	Muscle Satellite Cultured Cells	--
20	chr11:120308400-120357800	Strong transcription	Adipose Nuclei	Adipose
21	chr11:120309800-120333800	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:120310000-120336000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr11:120310200-120350600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:120310400-120358000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:120310800-120333800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr11:120311200-120357200	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr11:120312000-120328800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr11:120312000-120333800	Strong transcription	Skeletal Muscle Male	skeletal muscle
29	chr11:120312200-120333000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr11:120312200-120339000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:120312400-120326800	Strong transcription	HSMMtube	muscle
32	chr11:120312400-120328400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr11:120312400-120329800	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr11:120312400-120341800	Strong transcription	Fetal Muscle Leg	muscle
35	chr11:120312400-120351800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr11:120312400-120354000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr11:120312800-120334000	Strong transcription	Stomach Smooth Muscle	stomach
38	chr11:120312800-120357800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr11:120313000-120325800	Strong transcription	Colon Smooth Muscle	Colon
40	chr11:120314200-120362200	Strong transcription	Liver	Liver
41	chr11:120314800-120342000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr11:120315200-120353000	Strong transcription	Fetal Brain Female	brain
43	chr11:120315400-120329000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr11:120315400-120342400	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr11:120315600-120328400	Strong transcription	Brain Germinal Matrix	brain
46	chr11:120315800-120325600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr11:120315800-120325600	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr11:120315800-120326200	Strong transcription	Ovary	ovary
49	chr11:120315800-120326400	Strong transcription	Rectal Smooth Muscle	rectum
50	chr11:120315800-120328000	Strong transcription	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links