Variant report

Variant	rs17676332
Chromosome Location	chr15:41859499-41859500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1023193	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1079371	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070339	1.00[CHD][hapmap]
rs11630972	1.00[JPT][hapmap]
rs11634582	1.00[JPT][hapmap]
rs11635790	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11636523	1.00[JPT][hapmap]
rs11639399	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12148316	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906666	1.00[JPT][hapmap]
rs12917387	1.00[JPT][hapmap]
rs17677098	1.00[JPT][hapmap]
rs17677757	1.00[JPT][hapmap]
rs17678310	1.00[JPT][hapmap]
rs2178003	1.00[JPT][hapmap]
rs34040639	1.00[JPT][hapmap]
rs7167078	1.00[JPT][hapmap]
rs7171675	1.00[CHD][hapmap]
rs72739702	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72741804	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8024626	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026760	0.89[AMR][1000 genomes]
rs8042535	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042809	1.00[JPT][hapmap]
rs8043421	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9646193	1.00[JPT][hapmap]

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs17676332	LTK	cis	lung	GTEx
rs17676332	ITPKA	cis	parietal	SCAN
rs17676332	RPAP1	cis	parietal	SCAN
rs17676332	RPAP1	cis	multi-tissue	Pritchard
rs17676332	SPTBN5	cis	cerebellum	SCAN
rs17676332	CAPN3	cis	parietal	SCAN
rs17676332	MAPKBP1	cis	cerebellum	SCAN
rs17676332	NDUFAF1	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	chr15:41853400-41859800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr15:41853400-41870600	Weak transcription	Stomach Mucosa	stomach
16	chr15:41853600-41859800	Genic enhancers	H1 Cell Line	embryonic stem cell
17	chr15:41853600-41860000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:41853600-41862200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr15:41853800-41861400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:41853800-41864000	Genic enhancers	Brain Cingulate Gyrus	brain
21	chr15:41854000-41860200	Strong transcription	Dnd41	blood
22	chr15:41854000-41860800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr15:41854000-41871400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:41854200-41859600	Weak transcription	Pancreas	Pancrea
25	chr15:41854200-41877000	Weak transcription	Fetal Brain Male	brain
26	chr15:41855000-41861400	Genic enhancers	Brain Anterior Caudate	brain
27	chr15:41855200-41860000	Weak transcription	Gastric	stomach
28	chr15:41855400-41860200	Weak transcription	Esophagus	oesophagus
29	chr15:41855400-41862000	Weak transcription	NHLF	lung
30	chr15:41855400-41863400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:41855400-41864400	Genic enhancers	Brain Hippocampus Middle	brain
32	chr15:41855400-41877000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr15:41855400-41877200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr15:41855600-41860400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:41855600-41860600	Weak transcription	NH-A	brain
36	chr15:41856200-41859600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr15:41856200-41860000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:41856400-41861800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:41856800-41860400	Weak transcription	Lung	lung
40	chr15:41856800-41861400	Genic enhancers	Brain Angular Gyrus	brain
41	chr15:41857000-41860000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:41857000-41860800	Weak transcription	Brain Germinal Matrix	brain
43	chr15:41857200-41859800	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr15:41857200-41860400	Weak transcription	Right Ventricle	heart
45	chr15:41857200-41860800	Weak transcription	HSMMtube	muscle
46	chr15:41857200-41862200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:41857400-41859600	Weak transcription	Spleen	Spleen
48	chr15:41857400-41859800	Enhancers	HepG2	liver
49	chr15:41857400-41860400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:41857400-41864000	Genic enhancers	Brain Inferior Temporal Lobe	brain

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