Variant report

Variant	rs11635440
Chromosome Location	chr15:57573834-57573835
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	POU2F2	chr15:57573504-57574020	GM12878	blood:	n/a	n/a
2	POU2F2	chr15:57573570-57573904	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
TCF12	TF binding region
ENSG00000239035	TF binding region

Extended variants
information (count: 115 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs1037956	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1037958	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10518894	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10518895	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10518899	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs11071309	0.86[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11629653	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11630910	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11631084	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11632069	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11634352	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11636201	0.81[ASN][1000 genomes]
rs11636340	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11636348	0.81[ASN][1000 genomes]
rs11636919	0.80[ASN][1000 genomes]
rs11637955	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11852340	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11853331	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11855648	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11856073	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11857507	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11857722	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11858783	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs12050751	0.92[CEU][hapmap]
rs12899036	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12899588	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12901671	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12902099	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12902170	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12902581	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12903115	0.81[EUR][1000 genomes]
rs12903151	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12903221	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12904189	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12904321	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12904501	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12904561	0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12904602	0.85[CEU][hapmap]
rs12904634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12904933	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12906042	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12906335	0.86[ASN][1000 genomes]
rs12906566	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12908278	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12908760	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12909016	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12909696	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12910094	0.89[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12910109	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12910832	0.81[ASN][1000 genomes]
rs12911256	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12911297	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12911518	0.81[EUR][1000 genomes]
rs12912210	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12912353	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12912868	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12914425	0.96[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12914481	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12915489	0.94[CHB][hapmap];0.88[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12916478	0.81[EUR][1000 genomes]
rs12917093	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13313455	0.91[JPT][hapmap]
rs1462156	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs1545728	0.88[CEU][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17239431	0.86[EUR][1000 genomes]
rs17239508	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1814585	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1867641	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2169466	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs2278685	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290938	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2414491	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs2414492	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2431023	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2441925	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2593235	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2593237	0.84[ASN][1000 genomes]
rs2593238	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2615231	0.91[JPT][hapmap]
rs2733332	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs2733341	0.80[ASN][1000 genomes]
rs2951899	0.86[JPT][hapmap]
rs3095821	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3794613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4238321	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4238322	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4303429	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4353440	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4369592	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4447362	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4774250	0.86[CEU][hapmap];0.89[CHB][hapmap];0.86[JPT][hapmap]
rs4774251	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4774252	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4774910	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs4774913	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4774918	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4774919	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5014892	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61996955	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61996957	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62022237	0.81[ASN][1000 genomes]
rs6493901	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7161965	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7175436	0.91[JPT][hapmap]
rs745652	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8037901	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs898901	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs935326	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs960946	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs967514	0.91[JPT][hapmap]
rs978274	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];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	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv526342	chr15:57565859-57597280	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57520400-57576000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:57522800-57585000	Strong transcription	Fetal Thymus	thymus
3	chr15:57526600-57574200	Weak transcription	Hela-S3	cervix
4	chr15:57536800-57574200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:57537800-57598200	Weak transcription	Colonic Mucosa	Colon
6	chr15:57539400-57574800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:57544600-57574800	Weak transcription	Fetal Brain Male	brain
8	chr15:57546000-57580600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:57548200-57578000	Weak transcription	Fetal Heart	heart
10	chr15:57552200-57588600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr15:57552400-57578600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:57553200-57585000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:57556200-57580600	Weak transcription	Stomach Mucosa	stomach
14	chr15:57557000-57584600	Weak transcription	Colon Smooth Muscle	Colon
15	chr15:57557600-57578000	Weak transcription	Pancreas	Pancrea
16	chr15:57557600-57588600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:57562600-57575600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr15:57562600-57578000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:57562600-57584200	Strong transcription	Fetal Muscle Trunk	muscle
20	chr15:57562600-57584600	Strong transcription	Fetal Muscle Leg	muscle
21	chr15:57564000-57582400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr15:57564000-57583600	Strong transcription	Dnd41	blood
23	chr15:57564800-57575600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:57564800-57584600	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr15:57565000-57576400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:57565000-57583400	Strong transcription	Thymus	Thymus
27	chr15:57565200-57574600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:57565200-57575200	Strong transcription	Fetal Lung	lung
29	chr15:57565600-57584600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:57565800-57578000	Weak transcription	Right Ventricle	heart
31	chr15:57566000-57574400	Weak transcription	Brain Anterior Caudate	brain
32	chr15:57566000-57577800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr15:57566000-57577800	Weak transcription	Brain Substantia Nigra	brain
34	chr15:57566000-57579000	Weak transcription	Brain Germinal Matrix	brain
35	chr15:57566000-57584400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr15:57566000-57591600	Weak transcription	Esophagus	oesophagus
37	chr15:57566200-57578400	Weak transcription	Spleen	Spleen
38	chr15:57566400-57577800	Weak transcription	Small Intestine	intestine
39	chr15:57566400-57578000	Weak transcription	Ovary	ovary
40	chr15:57567000-57574800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr15:57567000-57579000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr15:57567400-57574000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr15:57567400-57575800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr15:57567400-57577600	Weak transcription	A549	lung
45	chr15:57567800-57578600	Weak transcription	NHEK	skin
46	chr15:57568000-57576000	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr15:57568000-57578200	Weak transcription	Brain Angular Gyrus	brain
48	chr15:57568000-57578400	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr15:57568000-57582600	Weak transcription	Aorta	Aorta
50	chr15:57568000-57588400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links