Variant report

Variant	rs514438
Chromosome Location	chr15:43620443-43620444
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:43619415-43621038	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:43618471-43623574	GM12891	blood:	n/a	n/a
3	POLR2A	chr15:43617884-43623229	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:43618045-43620940	K562	blood:	n/a	n/a
5	POLR2A	chr15:43620376-43621715	GM12878	blood:	n/a	n/a
6	POLR2A	chr15:43619431-43623219	K562	blood:	n/a	n/a
7	POLR2A	chr15:43620058-43623582	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr15:43618735-43620944	K562	blood:	n/a	n/a
9	POLR2A	chr15:43617486-43620882	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr15:43619221-43621507	HepG2	liver:	n/a	n/a
11	POLR2A	chr15:43620422-43621704	GM12892	blood:	n/a	n/a
12	POLR2A	chr15:43617177-43620881	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr15:43620050-43621275	HepG2	liver:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:43397435..43400079-chr15:43619938..43624138,3	K562	blood:
2	chr15:43620224..43622600-chr15:43663902..43665478,2	MCF-7	breast:
3	chr15:43586330..43589415-chr15:43618040..43621005,4	K562	blood:
4	chr15:43618581..43624264-chr15:43661265..43664929,7	MCF-7	breast:
5	chr15:43618584..43620563-chr15:43643035..43645762,2	K562	blood:
6	chr15:43586588..43588941-chr15:43618040..43620629,3	K562	blood:
7	chr15:43606393..43608534-chr15:43619037..43620672,2	MCF-7	breast:
8	chr15:43584770..43587744-chr15:43618210..43620882,2	MCF-7	breast:
9	chr15:43619535..43624096-chr15:43662038..43665421,4	K562	blood:
10	chr15:43571338..43574214-chr15:43618657..43622685,4	K562	blood:
11	chr15:43618225..43620863-chr15:43639470..43641474,2	K562	blood:
12	chr15:43477366..43479216-chr15:43620083..43621623,2	MCF-7	breast:

No data

Variant related genes	Relation type
ADAL	TF binding region
ENSG00000166946	Chromatin interaction
ENSG00000140265	Chromatin interaction
ENSG00000137822	Chromatin interaction
ENSG00000159459	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10518812	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12899865	1.00[CEU][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12900259	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12905220	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12906017	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs12906481	0.84[EUR][1000 genomes]
rs12907870	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12908460	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12911569	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12911740	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs12912744	1.00[CEU][hapmap];0.90[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap]
rs12913977	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12914122	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16957680	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16957715	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16957730	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17723479	0.95[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17780417	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17780920	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1814324	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2230451	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34002293	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34178146	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34181131	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34212866	0.82[EUR][1000 genomes]
rs34515241	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34591748	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34633582	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34657657	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34661349	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34697113	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34767197	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34860428	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34921640	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35158584	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35160541	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35278805	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35311230	0.85[EUR][1000 genomes]
rs35326382	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35681736	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35903301	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35958032	0.84[EUR][1000 genomes]
rs35975365	0.91[EUR][1000 genomes]
rs35992154	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36078097	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3862138	0.95[CEU][hapmap];0.81[MEX][hapmap]
rs55748552	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs55801120	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs60018990	0.80[EUR][1000 genomes]
rs62019432	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62019442	0.80[EUR][1000 genomes]
rs62020574	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62020575	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62021176	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62021180	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs66629206	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71476435	0.84[EUR][1000 genomes]
rs7168220	0.84[EUR][1000 genomes]
rs7173383	1.00[CEU][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7176923	0.95[CEU][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7177146	1.00[CEU][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs7177892	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7180812	1.00[CEU][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7181545	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7181634	1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7181783	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7182292	0.84[EUR][1000 genomes]
rs7183708	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72707530	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72709850	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8027748	0.88[AMR][1000 genomes];0.82[EUR][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	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv534649	chr15:43591116-43851142	Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1512	chr15:43616834-43661646	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs514438	WDR76	cis	parietal	SCAN
rs514438	ZNF690	cis	multi-tissue	Pritchard
rs514438	TUBGCP4	cis	cerebellum	SCAN
rs514438	ADAL	cis	cerebellum	SCAN
rs514438	ZSCAN29	cis	lymphoblastoid	seeQTL
rs514438	TGM7	cis	Esophagus Mucosa	GTEx
rs514438	TGM5	cis	lymphoblastoid	seeQTL
rs514438	LCMT2	cis	Esophagus Mucosa	GTEx
rs514438	ZFP106	cis	cerebellum	SCAN
rs514438	ZSCAN29	cis	multi-tissue	Pritchard

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43613000-43620600	Weak transcription	Right Atrium	heart
2	chr15:43615000-43621000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:43615600-43620600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:43615800-43620600	Weak transcription	Brain Substantia Nigra	brain
5	chr15:43616400-43620600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:43616400-43620600	Weak transcription	HSMM	muscle
7	chr15:43616800-43620600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr15:43616800-43620600	Weak transcription	Fetal Brain Male	brain
9	chr15:43617000-43620600	Weak transcription	Fetal Lung	lung
10	chr15:43617000-43621200	Weak transcription	Osteobl	bone
11	chr15:43617200-43620600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:43617200-43620800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:43617400-43620600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr15:43617600-43620600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr15:43617600-43620600	Weak transcription	A549	lung
16	chr15:43617800-43620600	Weak transcription	NHLF	lung
17	chr15:43617800-43620800	Enhancers	Psoas Muscle	Psoas
18	chr15:43618000-43620600	Weak transcription	Small Intestine	intestine
19	chr15:43618000-43620600	Weak transcription	GM12878-XiMat	blood
20	chr15:43618200-43620600	Weak transcription	Gastric	stomach
21	chr15:43618200-43620600	Weak transcription	HMEC	breast
22	chr15:43618200-43620800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr15:43618200-43621400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:43618400-43620600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr15:43618400-43620800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr15:43618600-43620600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr15:43618600-43620600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:43618600-43620600	Weak transcription	Adipose Nuclei	Adipose
29	chr15:43618600-43620600	Weak transcription	Left Ventricle	heart
30	chr15:43618800-43620600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:43618800-43620600	Weak transcription	NHEK	skin
32	chr15:43619000-43620600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:43619000-43620800	Weak transcription	Lung	lung
34	chr15:43619200-43620600	Weak transcription	Placenta	Placenta
35	chr15:43619200-43620600	Weak transcription	Fetal Stomach	stomach
36	chr15:43619200-43621200	Weak transcription	HSMMtube	muscle
37	chr15:43619400-43620600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr15:43619400-43620800	Genic enhancers	K562	blood
39	chr15:43619400-43621000	Enhancers	Colon Smooth Muscle	Colon
40	chr15:43619600-43620600	Strong transcription	Primary B cells from cord blood	blood
41	chr15:43619600-43620600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:43619600-43620600	Genic enhancers	Brain Germinal Matrix	brain
43	chr15:43619600-43620600	Weak transcription	Duodenum Mucosa	Duodenum
44	chr15:43619600-43620800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr15:43619600-43621000	Enhancers	Fetal Heart	heart
46	chr15:43619600-43621000	Strong transcription	Fetal Muscle Trunk	muscle
47	chr15:43619600-43621200	Genic enhancers	Primary T cells from cord blood	blood
48	chr15:43619600-43621200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr15:43619600-43621600	Enhancers	Ovary	ovary
50	chr15:43619800-43620600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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