Variant report

Variant	rs28374631
Chromosome Location	chr15:52620950-52620951
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr15:52620907-52621392	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52580244..52584410-chr15:52619433..52625902,7	MCF-7	breast:
2	chr15:52620021..52622500-chr15:52969872..52972000,2	MCF-7	breast:
3	chr15:52586610..52588635-chr15:52620259..52623836,3	MCF-7	breast:
4	chr15:52620335..52622038-chr15:52622788..52624501,2	K562	blood:
5	chr15:52586491..52591216-chr15:52616639..52620986,7	MCF-7	breast:

No data

Variant related genes	Relation type
MYO5A	TF binding region
ENSG00000047346	Chromatin interaction
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10518683	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10518688	1.00[EUR][1000 genomes]
rs1104800	0.96[ASN][1000 genomes]
rs1108808	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12101973	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12913979	0.96[ASN][1000 genomes]
rs13329278	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13329402	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13329417	1.00[EUR][1000 genomes]
rs13329500	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1669870	0.96[ASN][1000 genomes]
rs1669872	0.96[ASN][1000 genomes]
rs16964891	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16964903	1.00[EUR][1000 genomes]
rs16964910	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964915	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16964919	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964921	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964924	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16964927	1.00[EUR][1000 genomes]
rs16964928	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16964935	1.00[EUR][1000 genomes]
rs16964944	1.00[EUR][1000 genomes]
rs16964952	1.00[EUR][1000 genomes]
rs2242059	0.96[ASN][1000 genomes]
rs2414137	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414138	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2414145	0.96[ASN][1000 genomes]
rs28366864	1.00[EUR][1000 genomes]
rs28367336	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28367508	1.00[EUR][1000 genomes]
rs28409636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28409760	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28415069	1.00[EUR][1000 genomes]
rs28415349	1.00[EUR][1000 genomes]
rs28426997	1.00[EUR][1000 genomes]
rs28444393	1.00[EUR][1000 genomes]
rs28462026	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28475475	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28479614	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28480975	1.00[EUR][1000 genomes]
rs28488423	1.00[EUR][1000 genomes]
rs28496242	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28503750	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28508266	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28514341	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28515624	1.00[EUR][1000 genomes]
rs28532168	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28534436	1.00[EUR][1000 genomes]
rs28538563	1.00[EUR][1000 genomes]
rs28552981	1.00[EUR][1000 genomes]
rs28556657	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28564655	1.00[EUR][1000 genomes]
rs28590330	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28594692	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28605633	1.00[EUR][1000 genomes]
rs28618215	1.00[AMR][1000 genomes]
rs28633243	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28638475	1.00[EUR][1000 genomes]
rs28649737	1.00[EUR][1000 genomes]
rs28650960	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28653534	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655190	1.00[EUR][1000 genomes]
rs28657676	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28660682	1.00[EUR][1000 genomes]
rs28661501	1.00[EUR][1000 genomes]
rs28669685	1.00[AMR][1000 genomes]
rs28693941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28697879	1.00[EUR][1000 genomes]
rs28735959	1.00[EUR][1000 genomes]
rs28756182	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3764230	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4499185	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4624108	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774621	0.96[ASN][1000 genomes]
rs4987194	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57864537	1.00[EUR][1000 genomes]
rs58029714	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58812575	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7163242	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7163778	0.96[ASN][1000 genomes]
rs7164164	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7164722	1.00[EUR][1000 genomes]
rs7164872	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7166034	1.00[EUR][1000 genomes]
rs7167181	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7167437	0.85[ASN][1000 genomes]
rs7167680	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7167890	0.91[AMR][1000 genomes]
rs7167916	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7168076	1.00[EUR][1000 genomes]
rs7168251	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169104	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7169346	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7170622	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7171999	0.96[ASN][1000 genomes]
rs7178069	1.00[EUR][1000 genomes]
rs7179156	1.00[EUR][1000 genomes]
rs7182148	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73408408	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73408415	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73408465	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73408469	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73408478	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73410713	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73410715	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73410759	1.00[EUR][1000 genomes]
rs744501	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8023623	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8024412	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8024624	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8027637	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8027777	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030307	0.96[ASN][1000 genomes]
rs8035199	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040369	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040558	0.98[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs8041819	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8042235	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8042245	0.92[AMR][1000 genomes]
rs876549	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9744852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920739	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920749	1.00[EUR][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	esv1846455	chr15:52501831-52714452	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52595800-52628800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr15:52596200-52623600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr15:52597800-52629600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr15:52597800-52643400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr15:52600600-52624200	Weak transcription	Liver	Liver
6	chr15:52600800-52622800	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr15:52600800-52646600	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr15:52601000-52622600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr15:52601000-52643400	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr15:52601200-52622600	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr15:52601600-52622400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr15:52601600-52622800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:52601800-52621400	Weak transcription	Psoas Muscle	Psoas
14	chr15:52602000-52622800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:52602200-52622600	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr15:52602600-52622800	Strong transcription	Primary B cells from peripheral blood	blood
17	chr15:52605400-52622800	Strong transcription	HSMMtube	muscle
18	chr15:52607000-52622800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
20	chr15:52608600-52622400	Strong transcription	GM12878-XiMat	blood
21	chr15:52608600-52629200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr15:52609000-52623600	Weak transcription	Hela-S3	cervix
23	chr15:52609800-52622000	Weak transcription	Osteobl	bone
24	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr15:52610000-52643400	Weak transcription	Placenta	Placenta
26	chr15:52611400-52623600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr15:52611400-52629400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:52611600-52621000	Weak transcription	Right Atrium	heart
29	chr15:52611600-52621200	Weak transcription	NHDF-Ad	bronchial
30	chr15:52611600-52621600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr15:52611600-52621800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr15:52611600-52629800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr15:52611600-52650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:52611800-52623600	Weak transcription	A549	lung
35	chr15:52611800-52623800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr15:52611800-52675800	Weak transcription	Gastric	stomach
37	chr15:52613000-52642600	Weak transcription	Colon Smooth Muscle	Colon
38	chr15:52613200-52621200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr15:52613600-52623600	Strong transcription	HUVEC	blood vessel
40	chr15:52613600-52666600	Weak transcription	Right Ventricle	heart
41	chr15:52613800-52623800	Weak transcription	Fetal Heart	heart
42	chr15:52614000-52621400	Weak transcription	Ovary	ovary
43	chr15:52614600-52622000	Weak transcription	Thymus	Thymus
44	chr15:52614800-52621400	Weak transcription	HSMM	muscle
45	chr15:52614800-52623800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:52614800-52623800	Weak transcription	Brain Angular Gyrus	brain
47	chr15:52614800-52642600	Weak transcription	Esophagus	oesophagus
48	chr15:52614800-52653200	Weak transcription	Colonic Mucosa	Colon
49	chr15:52616200-52621800	Strong transcription	NHEK	skin
50	chr15:52616400-52622800	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links