Variant report

Variant	rs11169058
Chromosome Location	chr12:49924637-49924638
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49923572..49927432-chr12:49929998..49933415,4	K562	blood:
2	chr12:49744876..49747449-chr12:49923106..49924717,2	MCF-7	breast:
3	chr12:49657840..49660330-chr12:49922519..49924856,2	K562	blood:

Variant related genes	Relation type
ENSG00000167553	Chromatin interaction
ENSG00000135519	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000178401	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10160947	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10161131	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10506284	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10506285	1.00[JPT][hapmap]
rs10783314	1.00[YRI][hapmap]
rs10875955	0.82[AMR][1000 genomes]
rs11168981	1.00[JPT][hapmap]
rs11169005	0.94[ASW][hapmap];1.00[GIH][hapmap];0.87[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs11169008	1.00[YRI][hapmap]
rs11169015	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11169016	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11169017	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11169027	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11169043	0.83[AFR][1000 genomes]
rs11169045	0.82[AFR][1000 genomes]
rs11169048	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169049	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169059	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169063	0.94[ASW][hapmap];0.91[CEU][hapmap];0.94[GIH][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes]
rs11611743	0.83[EUR][1000 genomes]
rs11834161	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12296440	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12299282	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12300817	1.00[ASN][1000 genomes]
rs12301632	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12305716	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12306118	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12306212	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12306430	1.00[CHD][hapmap]
rs12306481	1.00[CHD][hapmap]
rs12306645	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12306866	1.00[JPT][hapmap]
rs12309053	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12310129	1.00[JPT][hapmap]
rs12314428	1.00[ASN][1000 genomes]
rs12315996	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12316170	1.00[ASN][1000 genomes]
rs12318633	1.00[ASN][1000 genomes]
rs12320284	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12322561	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12322571	1.00[ASN][1000 genomes]
rs12581343	1.00[CHB][hapmap]
rs1317131	1.00[CHD][hapmap]
rs17123696	1.00[JPT][hapmap]
rs17123751	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17123764	1.00[CHD][hapmap]
rs17123790	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17123865	1.00[CHB][hapmap]
rs17197593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1874910	1.00[JPT][hapmap]
rs2270741	1.00[JPT][hapmap]
rs2272478	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144469	1.00[JPT][hapmap]
rs4569075	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4641552	1.00[CHD][hapmap]
rs4898506	0.85[YRI][hapmap]
rs57200170	1.00[ASN][1000 genomes]
rs57601151	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58125498	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs60808917	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580707	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap]
rs6580709	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs6580716	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7132684	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7133398	0.88[ASW][hapmap];0.90[GIH][hapmap];0.84[TSI][hapmap];0.85[YRI][hapmap]
rs7139061	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7294648	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294973	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7295162	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7295556	0.88[ASW][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs7309997	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73297209	0.83[EUR][1000 genomes]
rs73301240	1.00[ASN][1000 genomes]
rs73301259	1.00[ASN][1000 genomes]
rs7342365	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7955541	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs7962951	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7963954	0.84[GIH][hapmap]
rs7965658	0.87[GIH][hapmap]
rs7969010	0.83[EUR][1000 genomes]
rs7969099	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs7974420	0.94[ASW][hapmap];1.00[GIH][hapmap];0.93[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap]
rs7975712	0.94[ASW][hapmap];0.90[CEU][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7976165	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7980731	0.94[ASW][hapmap];0.87[GIH][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap]
rs9919739	0.83[ASN][1000 genomes]
rs9919740	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs9919807	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv899070	chr12:49811311-49941500	Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv832406	chr12:49860693-50062136	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	nsv518746	chr12:49870964-49924637	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv482795	chr12:49897633-50068686	Flanking Active TSS Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	esv1801776	chr12:49915354-49934565	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49888800-49927800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:49905200-49927000	Weak transcription	Fetal Heart	heart
3	chr12:49909600-49925600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr12:49912600-49926400	Strong transcription	Fetal Muscle Trunk	muscle
5	chr12:49914400-49931400	Weak transcription	Pancreas	Pancrea
6	chr12:49915000-49925600	Weak transcription	Small Intestine	intestine
7	chr12:49916400-49931200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:49916800-49927200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:49917600-49931200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr12:49919200-49925400	Weak transcription	Liver	Liver
11	chr12:49919400-49925600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:49919800-49924800	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:49920000-49924800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:49920000-49928800	Weak transcription	Primary B cells from cord blood	blood
15	chr12:49920000-49931200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:49920200-49927400	Weak transcription	HepG2	liver
17	chr12:49920200-49928600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:49920200-49929600	Weak transcription	HMEC	breast
19	chr12:49920200-49931400	Weak transcription	Brain Anterior Caudate	brain
20	chr12:49920400-49925000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:49920400-49925800	Weak transcription	Colonic Mucosa	Colon
22	chr12:49920400-49929600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:49920400-49930000	Weak transcription	Brain Substantia Nigra	brain
24	chr12:49920600-49924800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:49920600-49925200	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:49920600-49925400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:49920600-49925600	Weak transcription	Thymus	Thymus
28	chr12:49920600-49926600	Weak transcription	Fetal Thymus	thymus
29	chr12:49920600-49926600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr12:49920600-49931200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr12:49920600-49931400	Weak transcription	Spleen	Spleen
32	chr12:49920800-49929600	Weak transcription	Fetal Brain Female	brain
33	chr12:49921200-49929600	Weak transcription	Placenta	Placenta
34	chr12:49921400-49927200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:49921600-49925200	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr12:49921600-49926400	Weak transcription	Primary T cells from cord blood	blood
37	chr12:49921800-49925000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr12:49921800-49925000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr12:49921800-49926000	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr12:49921800-49926400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr12:49921800-49926600	Weak transcription	Gastric	stomach
42	chr12:49921800-49926800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:49921800-49927200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr12:49921800-49928200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:49921800-49928400	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr12:49921800-49928600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr12:49921800-49928600	Weak transcription	Brain Germinal Matrix	brain
48	chr12:49921800-49928800	Weak transcription	Brain Hippocampus Middle	brain
49	chr12:49921800-49929600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:49921800-49930200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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