Variant report

Variant	rs2305419
Chromosome Location	chr15:52622757-52622758
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52621764..52624675-chr15:52941173..52943708,2	MCF-7	breast:
2	chr15:52580244..52584410-chr15:52619433..52625902,7	MCF-7	breast:
3	chr15:52622486..52625746-chr15:52626312..52630161,4	MCF-7	breast:
4	chr15:52622541..52625275-chr15:52625707..52627338,3	MCF-7	breast:
5	chr15:52586610..52588635-chr15:52620259..52623836,3	MCF-7	breast:
6	chr15:52622204..52624177-chr15:52820582..52822352,2	MCF-7	breast:
7	chr15:52622362..52624417-chr15:52969873..52971503,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197535	Chromatin interaction
ENSG00000128833	Chromatin interaction
ENSG00000259935	Chromatin interaction
ENSG00000047346	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1104800	1.00[CHB][hapmap]
rs13329402	1.00[CHB][hapmap]
rs16964915	1.00[CHB][hapmap]
rs2242059	1.00[CHB][hapmap]
rs2242060	1.00[JPT][hapmap]
rs2305420	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2414138	1.00[CHB][hapmap]
rs2414143	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3751615	1.00[JPT][hapmap];0.86[AFR][1000 genomes]
rs3751617	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3751618	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3794562	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4528514	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs4624108	1.00[CHB][hapmap]
rs4625671	1.00[YRI][hapmap]
rs7168251	1.00[CHB][hapmap]
rs8030307	1.00[CHB][hapmap]
rs8040369	1.00[CHB][hapmap]
rs9920739	1.00[CHB][hapmap]

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:110 , 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	chr15:52601000-52643400	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr15:52601600-52622800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr15:52602000-52622800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:52602600-52622800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr15:52605400-52622800	Strong transcription	HSMMtube	muscle
13	chr15:52607000-52622800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
15	chr15:52608600-52629200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:52609000-52623600	Weak transcription	Hela-S3	cervix
17	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:52610000-52643400	Weak transcription	Placenta	Placenta
19	chr15:52611400-52623600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr15:52611400-52629400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:52611600-52629800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:52611600-52650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:52611800-52623600	Weak transcription	A549	lung
24	chr15:52611800-52623800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr15:52611800-52675800	Weak transcription	Gastric	stomach
26	chr15:52613000-52642600	Weak transcription	Colon Smooth Muscle	Colon
27	chr15:52613600-52623600	Strong transcription	HUVEC	blood vessel
28	chr15:52613600-52666600	Weak transcription	Right Ventricle	heart
29	chr15:52613800-52623800	Weak transcription	Fetal Heart	heart
30	chr15:52614800-52623800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:52614800-52623800	Weak transcription	Brain Angular Gyrus	brain
32	chr15:52614800-52642600	Weak transcription	Esophagus	oesophagus
33	chr15:52614800-52653200	Weak transcription	Colonic Mucosa	Colon
34	chr15:52616400-52622800	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr15:52616800-52631800	Weak transcription	Fetal Stomach	stomach
36	chr15:52618200-52622800	Strong transcription	Primary T cells from cord blood	blood
37	chr15:52619000-52623600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr15:52619200-52623800	Weak transcription	NH-A	brain
39	chr15:52619200-52632000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr15:52619600-52623600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr15:52619600-52632000	Weak transcription	Brain Germinal Matrix	brain
42	chr15:52619800-52628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:52619800-52640600	Weak transcription	Left Ventricle	heart
44	chr15:52619800-52641200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:52620000-52623600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr15:52620000-52623600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr15:52620000-52629000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr15:52620000-52632000	Weak transcription	Lung	lung
49	chr15:52620000-52652200	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr15:52620200-52623600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links