Variant report

Variant	rs62015997
Chromosome Location	chr15:52618275-52618276
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52588592..52591389-chr15:52616292..52618634,2	K562	blood:
2	chr15:52580122..52582567-chr15:52617504..52619991,4	MCF-7	breast:
3	chr15:52586746..52588342-chr15:52615809..52618694,2	MCF-7	breast:
4	chr15:52616858..52619301-chr15:52859591..52861409,2	MCF-7	breast:
5	chr15:52586491..52591216-chr15:52616639..52620986,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128989	Chromatin interaction
ENSG00000128833	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10444827	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10851513	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11633035	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637651	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11638118	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11638675	0.88[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12593858	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1626180	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1632403	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1669859	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1669865	0.86[AFR][1000 genomes]
rs1669871	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1669875	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1669876	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1724584	0.86[AFR][1000 genomes]
rs1724617	0.86[AFR][1000 genomes]
rs1724640	0.86[AFR][1000 genomes]
rs1967624	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2444012	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2444014	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2444017	0.86[AFR][1000 genomes]
rs2462855	0.86[AFR][1000 genomes]
rs2693459	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59277991	0.86[AFR][1000 genomes]
rs62015995	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62016004	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62016006	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8031817	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8035295	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][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	chr15:52606800-52618600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr15:52607000-52622800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
21	chr15:52608600-52622400	Strong transcription	GM12878-XiMat	blood
22	chr15:52608600-52629200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:52609000-52619600	Weak transcription	HepG2	liver
24	chr15:52609000-52623600	Weak transcription	Hela-S3	cervix
25	chr15:52609600-52618600	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:52609800-52622000	Weak transcription	Osteobl	bone
27	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:52610000-52643400	Weak transcription	Placenta	Placenta
29	chr15:52611400-52620600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:52611400-52623600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr15:52611400-52629400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:52611600-52618600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr15:52611600-52618600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr15:52611600-52618600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr15:52611600-52620200	Weak transcription	Fetal Brain Male	brain
36	chr15:52611600-52620800	Weak transcription	Pancreas	Pancrea
37	chr15:52611600-52621000	Weak transcription	Right Atrium	heart
38	chr15:52611600-52621200	Weak transcription	NHDF-Ad	bronchial
39	chr15:52611600-52621600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:52611600-52621800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr15:52611600-52629800	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr15:52611600-52650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:52611800-52619400	Weak transcription	H1 Cell Line	embryonic stem cell
44	chr15:52611800-52619600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr15:52611800-52623600	Weak transcription	A549	lung
46	chr15:52611800-52623800	Weak transcription	Duodenum Mucosa	Duodenum
47	chr15:52611800-52675800	Weak transcription	Gastric	stomach
48	chr15:52612600-52618600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr15:52612800-52618600	Weak transcription	Brain Substantia Nigra	brain
50	chr15:52612800-52618600	Weak transcription	Sigmoid Colon	Sigmoid Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links