Variant report

Variant	rs16872362
Chromosome Location	chr5:74159157-74159158
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr5:74158979-74159243	HepG2	liver:	n/a	chr5:74159118-74159129
2	POLR2A	chr5:74159106-74159641	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:73983818..73985346-chr5:74157692..74159898,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271714	TF binding region

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];0.85[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];0.89[YRI][hapmap];0.83[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];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872349	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	0.96[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	0.94[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	0.94[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];0.88[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	0.93[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	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764669	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764675	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764676	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764683	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764684	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764687	0.96[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
rs16872362	TINP1	Cis_1M	lymphoblastoid	RTeQTL
rs16872362	TINP1	cis	lesional skin	skin_eQTL
rs16872362	TINP1	cis	normal skin	skin_eQTL
rs16872362	NSA2	cis	lung	GTEx
rs16872362	NSA2	cis	Nerve Tibial	GTEx
rs16872362	NSA2	cis	Heart Left Ventricle	GTEx
rs16872362	NSA2	cis	Adipose Subcutaneous	GTEx
rs16872362	NSA2	cis	Esophagus Muscularis	GTEx
rs16872362	NSA2	cis	Artery Aorta	GTEx
rs16872362	NSA2	cis	Esophagus Mucosa	GTEx
rs16872362	NSA2	cis	Stomach	GTEx
rs16872362	NSA2	cis	Whole Blood	GTEx
rs16872362	TINP1	cis	uninvolved skin	skin_eQTL
rs16872362	TINP1	cis	multi-tissue	Pritchard
rs16872362	NSA2	cis	Muscle Skeletal	GTEx
rs16872362	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs16872362	NSA2	cis	Thyroid	GTEx
rs16872362	NSA2	cis	Artery Tibial	GTEx

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74140600-74160000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:74147400-74161000	Weak transcription	Primary T cells from cord blood	blood
3	chr5:74148200-74161200	Weak transcription	Right Atrium	heart
4	chr5:74148600-74159400	Weak transcription	HMEC	breast
5	chr5:74148600-74159800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr5:74148800-74160000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:74148800-74160600	Weak transcription	A549	lung
8	chr5:74148800-74160800	Weak transcription	Primary hematopoietic stem cells	blood
9	chr5:74149400-74160600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr5:74149400-74160800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:74153400-74159600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:74156400-74159600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr5:74157200-74161000	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr5:74157400-74159400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr5:74157600-74159200	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr5:74157800-74159400	Weak transcription	NHEK	skin
17	chr5:74157800-74159600	Enhancers	Brain Anterior Caudate	brain
18	chr5:74157800-74160000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
19	chr5:74157800-74160000	Enhancers	Brain Hippocampus Middle	brain
20	chr5:74157800-74160800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:74158000-74159200	Enhancers	Brain Cingulate Gyrus	brain
22	chr5:74158000-74160000	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr5:74158000-74160200	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr5:74158200-74159400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr5:74158200-74159600	Weak transcription	Fetal Brain Male	brain
26	chr5:74158200-74160200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr5:74158400-74159400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr5:74158400-74159400	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr5:74158400-74159400	Weak transcription	Dnd41	blood
30	chr5:74158400-74160200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr5:74158600-74159200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:74158600-74159400	Weak transcription	Brain Substantia Nigra	brain
33	chr5:74158600-74160400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:74158600-74161000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr5:74158600-74163000	Active TSS	H1 Cell Line	embryonic stem cell
36	chr5:74158800-74159400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr5:74158800-74163800	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr5:74159000-74159200	Active TSS	HUES48 Cell Line	embryonic stem cell
39	chr5:74159000-74159200	Active TSS	iPS-20b Cell Line	embryonic stem cell
40	chr5:74159000-74159800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr5:74159000-74160000	Flanking Active TSS	HepG2	liver
42	chr5:74159000-74160400	Weak transcription	Brain Angular Gyrus	brain
43	chr5:74159000-74160400	Enhancers	Pancreatic Islets	Pancreatic Islet
44	chr5:74159000-74162800	Active TSS	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links