Variant report

Variant	rs16872349
Chromosome Location	chr5:74152437-74152438
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1048167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10515192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10515194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10515199	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11959570	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872259	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872362	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561738	1.00[ASN][1000 genomes]
rs55899032	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55920995	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56127814	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56192858	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56203772	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57202395	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57549677	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58864890	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60492282	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6453076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6453079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6453082	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6861935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6870806	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6877188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6881400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6882035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883278	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883420	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6884338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6894177	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6898684	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764630	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764643	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764647	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764648	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764650	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764654	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764655	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764656	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764657	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764663	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764669	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764675	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764676	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764687	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764690	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72766504	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705519	0.90[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes]
rs7713812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7732440	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7732843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs957680	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9765469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs16872349	TINP1	Cis_1M	lymphoblastoid	RTeQTL
rs16872349	NSA2	cis	Heart Left Ventricle	GTEx
rs16872349	TINP1	cis	uninvolved skin	skin_eQTL
rs16872349	NSA2	cis	Adipose Subcutaneous	GTEx
rs16872349	NSA2	cis	Whole Blood	GTEx
rs16872349	NSA2	cis	Muscle Skeletal	GTEx
rs16872349	TINP1	cis	lesional skin	skin_eQTL
rs16872349	NSA2	cis	Esophagus Muscularis	GTEx
rs16872349	NSA2	cis	Stomach	GTEx
rs16872349	NSA2	cis	Artery Aorta	GTEx
rs16872349	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs16872349	NSA2	cis	Artery Tibial	GTEx
rs16872349	NSA2	cis	Esophagus Mucosa	GTEx
rs16872349	NSA2	cis	lung	GTEx
rs16872349	NSA2	cis	Nerve Tibial	GTEx
rs16872349	TINP1	cis	normal skin	skin_eQTL
rs16872349	NSA2	cis	Thyroid	GTEx
rs16872349	TINP1	cis	multi-tissue	Pritchard

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74069000-74153000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:74140200-74157800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:74140600-74160000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:74147400-74161000	Weak transcription	Primary T cells from cord blood	blood
5	chr5:74148200-74161200	Weak transcription	Right Atrium	heart
6	chr5:74148400-74158000	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:74148600-74156800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr5:74148600-74158000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr5:74148600-74159400	Weak transcription	HMEC	breast
10	chr5:74148600-74159800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr5:74148800-74160000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr5:74148800-74160600	Weak transcription	A549	lung
13	chr5:74148800-74160800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr5:74149000-74157600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:74149000-74157600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr5:74149200-74155800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:74149400-74157800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr5:74149400-74160600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr5:74149400-74160800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr5:74150600-74153400	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
21	chr5:74151200-74152600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr5:74151200-74153200	Strong transcription	HUES64 Cell Line	embryonic stem cell
23	chr5:74151400-74153400	Strong transcription	HepG2	liver
24	chr5:74151400-74158000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr5:74152000-74156600	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr5:74152000-74157200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:74152400-74153000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr5:74152400-74156800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr5:74152400-74157800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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