Variant report

Variant	rs17118461
Chromosome Location	chr12:56687805-56687806
allele	C/T
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	chr12:56687790-56687857	HepG2	liver:	n/a	n/a
2	POLR2A	chr12:56687576-56687854	HepG2	liver:	n/a	n/a
3	POLR2A	chr12:56687550-56687877	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
CS	TF binding region

Extended variants
information (count: 79 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10876882	0.94[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs10876885	1.00[EUR][1000 genomes]
rs1091527	1.00[EUR][1000 genomes]
rs11171812	0.83[AFR][1000 genomes]
rs11171818	1.00[EUR][1000 genomes]
rs11171819	1.00[EUR][1000 genomes]
rs11171822	1.00[EUR][1000 genomes]
rs11575221	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.82[YRI][hapmap];1.00[EUR][1000 genomes]
rs11575236	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11830379	1.00[EUR][1000 genomes]
rs11832580	1.00[EUR][1000 genomes]
rs11833064	1.00[EUR][1000 genomes]
rs11834948	1.00[EUR][1000 genomes]
rs11835018	1.00[EUR][1000 genomes]
rs11835310	1.00[EUR][1000 genomes]
rs12306512	1.00[EUR][1000 genomes]
rs12318887	1.00[EUR][1000 genomes]
rs12322356	1.00[EUR][1000 genomes]
rs1274493	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs1626158	1.00[EUR][1000 genomes]
rs1689517	1.00[EUR][1000 genomes]
rs1689518	1.00[EUR][1000 genomes]
rs1702872	1.00[EUR][1000 genomes]
rs17118590	1.00[EUR][1000 genomes]
rs1918496	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2020854	0.89[ASW][hapmap];0.85[LWK][hapmap];0.93[MKK][hapmap];0.89[YRI][hapmap]
rs2035948	1.00[EUR][1000 genomes]
rs2066808	0.94[ASW][hapmap];0.89[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2371494	0.94[ASW][hapmap];0.93[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2629445	1.00[EUR][1000 genomes]
rs2629447	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs2640566	1.00[EUR][1000 genomes]
rs2643623	0.96[AFR][1000 genomes]
rs2643626	0.89[ASW][hapmap];0.93[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs2661728	1.00[EUR][1000 genomes]
rs2661729	1.00[EUR][1000 genomes]
rs2695782	0.89[ASW][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs2695788	0.94[AFR][1000 genomes]
rs2695789	0.89[ASW][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes]
rs2934152	1.00[EUR][1000 genomes]
rs4301822	1.00[MEX][hapmap];1.00[EUR][1000 genomes]
rs4417324	1.00[EUR][1000 genomes]
rs56696262	1.00[EUR][1000 genomes]
rs57237559	1.00[EUR][1000 genomes]
rs57387549	1.00[EUR][1000 genomes]
rs58349500	1.00[EUR][1000 genomes]
rs59286728	1.00[EUR][1000 genomes]
rs59794023	1.00[EUR][1000 genomes]
rs61733171	1.00[EUR][1000 genomes]
rs61733875	1.00[EUR][1000 genomes]
rs6581093	1.00[EUR][1000 genomes]
rs703830	0.93[AFR][1000 genomes]
rs72478990	1.00[EUR][1000 genomes]
rs7298109	1.00[EUR][1000 genomes]
rs7300292	1.00[EUR][1000 genomes]
rs7304690	1.00[EUR][1000 genomes]
rs7309327	1.00[EUR][1000 genomes]
rs7310292	1.00[EUR][1000 genomes]
rs73324336	0.83[AFR][1000 genomes]
rs73324353	1.00[EUR][1000 genomes]
rs73324358	1.00[EUR][1000 genomes]
rs73338377	1.00[EUR][1000 genomes]
rs73338385	1.00[EUR][1000 genomes]
rs74094726	1.00[EUR][1000 genomes]
rs773652	0.89[ASW][hapmap];0.93[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs773664	0.92[AFR][1000 genomes]
rs773665	0.89[ASW][hapmap];0.89[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7954155	1.00[EUR][1000 genomes]
rs7954200	1.00[EUR][1000 genomes]
rs7957187	1.00[EUR][1000 genomes]
rs7958958	1.00[EUR][1000 genomes]
rs7962107	1.00[EUR][1000 genomes]
rs7975405	1.00[EUR][1000 genomes]
rs7977692	1.00[EUR][1000 genomes]
rs7979812	1.00[EUR][1000 genomes]
rs808919	0.98[LWK][hapmap];0.93[MKK][hapmap];0.89[YRI][hapmap]
rs901073	0.96[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56662000-56690000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr12:56662400-56692400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:56662600-56690000	Strong transcription	Fetal Muscle Leg	muscle
4	chr12:56663000-56692600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:56669600-56692800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr12:56676600-56693000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:56676800-56693200	Weak transcription	Aorta	Aorta
8	chr12:56677200-56692400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr12:56677800-56693200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr12:56680000-56691600	Weak transcription	Brain Angular Gyrus	brain
11	chr12:56680000-56693200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr12:56680200-56692200	Weak transcription	NHDF-Ad	bronchial
13	chr12:56680800-56690000	Weak transcription	Brain Hippocampus Middle	brain
14	chr12:56680800-56692200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr12:56681000-56692000	Weak transcription	Pancreas	Pancrea
16	chr12:56681000-56692200	Weak transcription	Esophagus	oesophagus
17	chr12:56681200-56688400	Weak transcription	Right Atrium	heart
18	chr12:56681200-56690200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr12:56681200-56693200	Weak transcription	Ovary	ovary
20	chr12:56681800-56691800	Strong transcription	Fetal Muscle Trunk	muscle
21	chr12:56682200-56688800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:56683000-56690400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:56683200-56691600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
24	chr12:56683400-56688000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr12:56683800-56690200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:56684000-56689000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:56684200-56688000	Strong transcription	GM12878-XiMat	blood
28	chr12:56684200-56688600	Strong transcription	Dnd41	blood
29	chr12:56684800-56688600	Strong transcription	K562	blood
30	chr12:56685000-56688000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:56685400-56688400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr12:56685600-56688800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr12:56685600-56690000	Weak transcription	Brain Germinal Matrix	brain
34	chr12:56685600-56690200	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:56685600-56690400	Weak transcription	Gastric	stomach
36	chr12:56685600-56690400	Weak transcription	HUVEC	blood vessel
37	chr12:56685600-56690600	Weak transcription	HUES64 Cell Line	embryonic stem cell
38	chr12:56685600-56690600	Weak transcription	HSMM	muscle
39	chr12:56685600-56690800	Weak transcription	Rectal Smooth Muscle	rectum
40	chr12:56685600-56691600	Weak transcription	Fetal Brain Female	brain
41	chr12:56685600-56691600	Weak transcription	Fetal Intestine Large	intestine
42	chr12:56685600-56691800	Weak transcription	Lung	lung
43	chr12:56685600-56692200	Weak transcription	Brain Substantia Nigra	brain
44	chr12:56685600-56692200	Weak transcription	Fetal Lung	lung
45	chr12:56685600-56692400	Weak transcription	HSMMtube	muscle
46	chr12:56685600-56692800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr12:56685600-56692800	Weak transcription	Fetal Kidney	kidney
48	chr12:56685800-56688400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:56685800-56688600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:56685800-56688800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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