Variant report

Variant	rs11169080
Chromosome Location	chr12:49980141-49980142
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49978768..49982908-chr12:50014945..50017649,3	MCF-7	breast:
2	chr12:49931802..49934765-chr12:49979240..49981760,2	K562	blood:
3	chr12:49979370..49981223-chr12:49986000..49987877,2	K562	blood:
4	chr12:49959724..49963152-chr12:49977588..49980958,4	K562	blood:
5	chr12:49970400..49973089-chr12:49977947..49980584,3	K562	blood:
6	chr12:49979616..49982528-chr12:49994555..49996212,2	MCF-7	breast:
7	chr12:49978538..49982226-chr12:49988172..49992676,4	K562	blood:
8	chr12:49960403..49963022-chr12:49980028..49982693,4	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000135519	Chromatin interaction
ENSG00000135436	Chromatin interaction
ENSG00000258284	Chromatin interaction
ENSG00000257964	Chromatin interaction
ENSG00000257243	Chromatin interaction
ENSG00000199237	Chromatin interaction
ENSG00000187778	Chromatin interaction
ENSG00000110844	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1049986	0.86[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap]
rs10875968	0.91[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11169005	1.00[CHB][hapmap]
rs11169008	1.00[CHB][hapmap]
rs11169043	0.81[ASN][1000 genomes]
rs11169045	0.81[ASN][1000 genomes]
rs11169063	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11169065	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs11169069	0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169070	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11169073	1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169076	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169081	0.83[ASW][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169082	1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169092	0.85[JPT][hapmap];0.83[YRI][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11169097	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.84[ASN][1000 genomes]
rs11169101	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11169104	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs11169106	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs11169140	0.91[CEU][hapmap];0.86[JPT][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1150057	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11615488	0.82[ASN][1000 genomes]
rs11615710	0.81[ASN][1000 genomes]
rs11833411	0.83[ASW][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11834380	1.00[CHD][hapmap];0.85[JPT][hapmap];0.93[MEX][hapmap]
rs12299505	1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12299513	0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12303310	0.85[JPT][hapmap]
rs12310510	0.85[JPT][hapmap]
rs12311527	0.84[ASN][1000 genomes]
rs12311839	0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12314878	0.89[ASN][1000 genomes]
rs12316284	0.85[JPT][hapmap];0.85[MEX][hapmap]
rs12320556	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12321819	1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.89[ASN][1000 genomes]
rs12322561	0.88[GIH][hapmap]
rs13066	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13906	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1470906	0.85[JPT][hapmap]
rs1574326	0.86[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs17123808	0.83[ASW][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17123981	0.91[CEU][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap]
rs1902329	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1902330	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2005195	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2241418	0.89[ASN][1000 genomes]
rs2278068	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2278069	0.93[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.89[ASN][1000 genomes]
rs2278070	0.87[ASN][1000 genomes]
rs2303305	0.93[CHD][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2336058	0.86[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs2878532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35275181	0.85[CHD][hapmap]
rs3815832	1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.89[ASN][1000 genomes]
rs3887727	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[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3887728	0.93[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4045193	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4073998	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4133070	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs4563	0.85[JPT][hapmap]
rs4584654	0.86[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs4993294	0.86[CHD][hapmap]
rs52824916	0.87[ASN][1000 genomes]
rs55853522	0.89[ASN][1000 genomes]
rs57916875	0.87[ASN][1000 genomes]
rs58125498	0.81[ASN][1000 genomes]
rs58278271	0.81[ASN][1000 genomes]
rs59233136	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs59940006	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61512987	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61616163	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7131915	0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7132792	0.93[CHD][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7133398	1.00[CHB][hapmap];0.86[CHD][hapmap]
rs7137976	0.86[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs7295556	0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs7296281	0.85[JPT][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7299609	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs7301209	0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs7306877	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7309607	0.83[EUR][1000 genomes]
rs7312658	0.83[EUR][1000 genomes]
rs73305008	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73305012	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7688	0.86[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs7952734	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs7952938	0.97[ASN][1000 genomes]
rs7953911	1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.89[ASN][1000 genomes]
rs7954994	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs7955586	0.88[CEU][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7956181	1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap]
rs7962863	0.82[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7963954	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7965658	0.83[ASW][hapmap];0.85[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7970241	1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.89[ASN][1000 genomes]
rs7973389	1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7975599	0.88[ASW][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.80[YRI][hapmap];0.89[ASN][1000 genomes]
rs7975712	1.00[CHB][hapmap];0.85[CHD][hapmap];0.81[ASN][1000 genomes]
rs7977389	1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.89[ASN][1000 genomes]
rs7979285	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980731	1.00[CHB][hapmap]
rs8626	0.88[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs876889	1.00[CHD][hapmap];0.85[JPT][hapmap];0.92[MEX][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs897056	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs933738	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
4	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49963000-49982200	Weak transcription	NHLF	lung
2	chr12:49963000-49984800	Weak transcription	Small Intestine	intestine
3	chr12:49963000-50003200	Weak transcription	Aorta	Aorta
4	chr12:49963200-49986800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr12:49963400-49984800	Weak transcription	Primary B cells from cord blood	blood
6	chr12:49967800-49987400	Weak transcription	Hela-S3	cervix
7	chr12:49971200-49984800	Weak transcription	Primary hematopoietic stem cells	blood
8	chr12:49972000-49982200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr12:49973800-49982400	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr12:49974400-49982400	Weak transcription	NHDF-Ad	bronchial
11	chr12:49974400-49983000	Weak transcription	Gastric	stomach
12	chr12:49974600-49982600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr12:49974800-49982000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr12:49974800-49983400	Weak transcription	Colonic Mucosa	Colon
15	chr12:49974800-49984600	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr12:49974800-49984800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr12:49974800-49984800	Weak transcription	Fetal Thymus	thymus
18	chr12:49974800-49985200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:49974800-49985800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr12:49974800-49986200	Weak transcription	K562	blood
21	chr12:49974800-49986600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr12:49974800-49986600	Weak transcription	NH-A	brain
23	chr12:49975000-49982400	Weak transcription	HMEC	breast
24	chr12:49975000-49982800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr12:49975000-49984800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr12:49975000-49986200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr12:49975000-49986400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr12:49975000-49987000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:49975400-49980200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr12:49975400-49983200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr12:49976000-49981600	Strong transcription	Primary T cells from cord blood	blood
32	chr12:49976000-49983200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
33	chr12:49976200-49980800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr12:49976400-49982200	Weak transcription	GM12878-XiMat	blood
35	chr12:49976400-49982400	Weak transcription	Psoas Muscle	Psoas
36	chr12:49976600-49981600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr12:49976600-49982200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr12:49976800-49981600	Weak transcription	A549	lung
39	chr12:49976800-49984200	Weak transcription	Fetal Intestine Large	intestine
40	chr12:49976800-49994000	Weak transcription	Liver	Liver
41	chr12:49977000-49982600	Strong transcription	Fetal Intestine Small	intestine
42	chr12:49977200-49980800	Strong transcription	NHEK	skin
43	chr12:49977200-49983000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr12:49977400-49980200	Strong transcription	Primary B cells from peripheral blood	blood
45	chr12:49977400-49980200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr12:49977400-49980200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr12:49977400-49981000	Strong transcription	Lung	lung
48	chr12:49977400-49982000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:49977600-49982000	Weak transcription	Pancreas	Pancrea
50	chr12:49977600-49982200	Weak transcription	Duodenum Smooth Muscle	Duodenum

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