Variant report

Variant	rs4519295
Chromosome Location	chr15:52623303-52623304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52548249..52549188-chr15:52622809..52623989,3	MCF-7	breast:
2	chr15:52621764..52624675-chr15:52941173..52943708,2	MCF-7	breast:
3	chr15:52580244..52584410-chr15:52619433..52625902,7	MCF-7	breast:
4	chr15:52623157..52624688-chr15:53027206..53029012,2	MCF-7	breast:
5	chr15:52548301..52549135-chr15:52623294..52624686,6	MCF-7	breast:
6	chr15:52622486..52625746-chr15:52626312..52630161,4	MCF-7	breast:
7	chr15:52623110..52623924-chr15:53027427..53028267,4	MCF-7	breast:
8	chr15:52622541..52625275-chr15:52625707..52627338,3	MCF-7	breast:
9	chr15:52586610..52588635-chr15:52620259..52623836,3	MCF-7	breast:
10	chr15:52623265..52623825-chr15:52892676..52893192,2	MCF-7	breast:
11	chr15:52623273..52624277-chr15:53027279..53028330,7	MCF-7	breast:
12	chr15:52622204..52624177-chr15:52820582..52822352,2	MCF-7	breast:
13	chr15:52620335..52622038-chr15:52622788..52624501,2	K562	blood:
14	chr15:52622362..52624417-chr15:52969873..52971503,2	MCF-7	breast:

No data

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

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1001522	0.84[CEU][hapmap];0.87[JPT][hapmap]
rs10083671	0.88[CEU][hapmap]
rs10083673	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs1009157	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10467925	1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10518687	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1125460	0.80[ASN][1000 genomes]
rs12324100	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12324121	1.00[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12914979	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1464963	0.88[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs1669858	0.85[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap]
rs1669867	0.89[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1724628	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs1724629	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs1724641	0.82[CEU][hapmap];0.86[JPT][hapmap]
rs17542017	0.80[ASN][1000 genomes]
rs2242057	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2242058	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2414150	0.96[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2414151	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs2444013	0.80[ASN][1000 genomes]
rs34926268	0.83[EUR][1000 genomes]
rs3858907	0.89[CEU][hapmap];0.80[ASN][1000 genomes]
rs4280181	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4606660	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4776037	0.87[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4776039	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62015999	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7176061	0.87[JPT][hapmap]
rs7176482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7176639	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7181109	0.83[EUR][1000 genomes]
rs7182150	0.96[CEU][hapmap];0.83[CHB][hapmap];0.87[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs752864	0.91[CHB][hapmap];0.84[JPT][hapmap];0.80[AMR][1000 genomes]
rs752865	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs752866	1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[EUR][1000 genomes]
rs8028033	0.96[CEU][hapmap];0.81[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8033626	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8038386	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs935892	0.85[CEU][hapmap];0.91[CHB][hapmap];0.93[JPT][hapmap];0.80[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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4519295	ARPP-19	Cis_1M	lymphoblastoid	RTeQTL
rs4519295	MYO5A	Cis_1M	lymphoblastoid	RTeQTL

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	chr15:52600800-52646600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr15:52601000-52643400	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr15:52607800-52657800	Weak transcription	Small Intestine	intestine
9	chr15:52608600-52629200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr15:52609000-52623600	Weak transcription	Hela-S3	cervix
11	chr15:52609800-52677600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:52610000-52643400	Weak transcription	Placenta	Placenta
13	chr15:52611400-52623600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:52611400-52629400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr15:52611600-52629800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr15:52611600-52650200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr15:52611800-52623600	Weak transcription	A549	lung
18	chr15:52611800-52623800	Weak transcription	Duodenum Mucosa	Duodenum
19	chr15:52611800-52675800	Weak transcription	Gastric	stomach
20	chr15:52613000-52642600	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:52613600-52623600	Strong transcription	HUVEC	blood vessel
22	chr15:52613600-52666600	Weak transcription	Right Ventricle	heart
23	chr15:52613800-52623800	Weak transcription	Fetal Heart	heart
24	chr15:52614800-52623800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr15:52614800-52623800	Weak transcription	Brain Angular Gyrus	brain
26	chr15:52614800-52642600	Weak transcription	Esophagus	oesophagus
27	chr15:52614800-52653200	Weak transcription	Colonic Mucosa	Colon
28	chr15:52616800-52631800	Weak transcription	Fetal Stomach	stomach
29	chr15:52619000-52623600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr15:52619200-52623800	Weak transcription	NH-A	brain
31	chr15:52619200-52632000	Weak transcription	Fetal Muscle Trunk	muscle
32	chr15:52619600-52623600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr15:52619600-52632000	Weak transcription	Brain Germinal Matrix	brain
34	chr15:52619800-52628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:52619800-52640600	Weak transcription	Left Ventricle	heart
36	chr15:52619800-52641200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:52620000-52623600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr15:52620000-52623600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr15:52620000-52629000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:52620000-52632000	Weak transcription	Lung	lung
41	chr15:52620000-52652200	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr15:52620200-52623600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr15:52620200-52623800	Weak transcription	Fetal Thymus	thymus
44	chr15:52620200-52624000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:52620200-52626400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:52620200-52626600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:52620200-52629600	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr15:52620400-52623800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr15:52620600-52623800	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr15:52620600-52659200	Weak transcription	Fetal Lung	lung

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