Variant report

Variant	rs6493005
Chromosome Location	chr15:41859152-41859153
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41849860..41852803-chr15:41858013..41860929,2	MCF-7	breast:
2	chr15:41853319..41856101-chr15:41857506..41859513,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000092445	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10438299	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs1200353	0.83[JPT][hapmap];0.87[MEX][hapmap]
rs12593920	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1473781	0.83[JPT][hapmap]
rs2246444	0.92[CHB][hapmap]
rs2277536	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2277537	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs2289743	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2412620	0.83[JPT][hapmap]
rs28655000	0.80[ASN][1000 genomes]
rs28657602	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3784283	0.92[CHB][hapmap]
rs4924552	0.94[ASN][1000 genomes]
rs4924554	0.86[ASN][1000 genomes]
rs4924556	0.92[CHB][hapmap];0.82[CHD][hapmap];0.83[JPT][hapmap]
rs4924559	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6493004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs6493005	RPAP1	cis	lymphoblastoid	seeQTL
rs6493005	C15orf23	cis	parietal	SCAN
rs6493005	JMJD7-PLA2G4B	cis	parietal	SCAN
rs6493005	JMJD7-PLA2G4B	cis	cerebellum	SCAN
rs6493005	C15orf62	cis	cerebellum	SCAN
rs6493005	SPTBN5	cis	cerebellum	SCAN
rs6493005	MAPKBP1	cis	cerebellum	SCAN
rs6493005	MGA	cis	lesional skin	skin_eQTL
rs6493005	RPAP1	cis	multi-tissue	Pritchard
rs6493005	RPAP1	cis	parietal	SCAN

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41852200-41877400	Weak transcription	Aorta	Aorta
2	chr15:41852400-41859600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:41852400-41860600	Weak transcription	HUVEC	blood vessel
4	chr15:41852400-41877200	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:41852600-41859600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:41852600-41877400	Weak transcription	HMEC	breast
7	chr15:41852800-41877400	Weak transcription	NHEK	skin
8	chr15:41853000-41861800	Genic enhancers	Fetal Intestine Large	intestine
9	chr15:41853000-41862000	Genic enhancers	Fetal Intestine Small	intestine
10	chr15:41853200-41860200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:41853200-41861800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
12	chr15:41853200-41863200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:41853200-41872600	Weak transcription	Hela-S3	cervix
14	chr15:41853400-41859400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
15	chr15:41853400-41859800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:41853400-41870600	Weak transcription	Stomach Mucosa	stomach
17	chr15:41853600-41859800	Genic enhancers	H1 Cell Line	embryonic stem cell
18	chr15:41853600-41860000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:41853600-41862200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr15:41853800-41861400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:41853800-41864000	Genic enhancers	Brain Cingulate Gyrus	brain
22	chr15:41854000-41860200	Strong transcription	Dnd41	blood
23	chr15:41854000-41860800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr15:41854000-41871400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr15:41854200-41859600	Weak transcription	Pancreas	Pancrea
26	chr15:41854200-41877000	Weak transcription	Fetal Brain Male	brain
27	chr15:41855000-41861400	Genic enhancers	Brain Anterior Caudate	brain
28	chr15:41855200-41860000	Weak transcription	Gastric	stomach
29	chr15:41855400-41860200	Weak transcription	Esophagus	oesophagus
30	chr15:41855400-41862000	Weak transcription	NHLF	lung
31	chr15:41855400-41863400	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr15:41855400-41864400	Genic enhancers	Brain Hippocampus Middle	brain
33	chr15:41855400-41877000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:41855400-41877200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:41855600-41860400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr15:41855600-41860600	Weak transcription	NH-A	brain
37	chr15:41856200-41859200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr15:41856200-41859600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr15:41856200-41860000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr15:41856400-41861800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr15:41856800-41860400	Weak transcription	Lung	lung
42	chr15:41856800-41861400	Genic enhancers	Brain Angular Gyrus	brain
43	chr15:41857000-41860000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:41857000-41860800	Weak transcription	Brain Germinal Matrix	brain
45	chr15:41857200-41859800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr15:41857200-41860400	Weak transcription	Right Ventricle	heart
47	chr15:41857200-41860800	Weak transcription	HSMMtube	muscle
48	chr15:41857200-41862200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:41857400-41859600	Weak transcription	Spleen	Spleen
50	chr15:41857400-41859800	Enhancers	HepG2	liver

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