Variant report

Variant	rs16872259
Chromosome Location	chr5:74068774-74068775
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:74063430..74066095-chr5:74068768..74070600,2	MCF-7	breast:
2	chr5:74068761..74070273-chr5:74071485..74073703,2	K562	blood:
3	chr5:74065827..74070020-chr5:74073603..74077107,4	MCF-7	breast:
4	chr5:74061790..74063907-chr5:74068318..74070016,2	MCF-7	breast:
5	chr5:74068532..74070395-chr5:74082418..74084693,2	K562	blood:

Variant related genes	Relation type
ENSG00000164347	Chromatin interaction
ENSG00000164346	Chromatin interaction
ENSG00000199645	Chromatin interaction

Extended variants
information (count: 63 )
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];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[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];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10515194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.99[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];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11959570	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.95[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];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872235	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872242	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16872323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16872345	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.94[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];1.00[AMR][1000 genomes];0.94[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];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17561738	1.00[ASN][1000 genomes]
rs55899032	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55920995	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56127814	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56192858	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56203772	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57202395	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57549677	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58864890	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs60492282	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[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];0.97[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];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6453082	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6861935	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]
rs6870806	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6873912	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6873998	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6877188	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6881400	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6883278	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6883420	0.91[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.93[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];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6894177	0.82[AMR][1000 genomes];0.95[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];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764630	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764643	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764647	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764648	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764650	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764654	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764655	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764656	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764657	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72764663	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764669	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764675	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764676	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764683	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764684	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764687	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72764690	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72766504	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705519	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs7713812	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7732440	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7732843	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs957680	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9765469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv598653	chr5:73992881-74095542	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs16872259	NSA2	cis	lung	GTEx
rs16872259	NSA2	cis	Stomach	GTEx
rs16872259	NSA2	cis	Muscle Skeletal	GTEx
rs16872259	TINP1	Cis_1M	lymphoblastoid	RTeQTL
rs16872259	TINP1	cis	uninvolved skin	skin_eQTL
rs16872259	NSA2	cis	Artery Aorta	GTEx
rs16872259	TINP1	cis	lesional skin	skin_eQTL
rs16872259	TINP1	cis	multi-tissue	Pritchard
rs16872259	NSA2	cis	Adipose Subcutaneous	GTEx
rs16872259	NSA2	cis	Skin Sun Exposed Lower leg	GTEx
rs16872259	NSA2	cis	Esophagus Muscularis	GTEx
rs16872259	NSA2	cis	Esophagus Mucosa	GTEx
rs16872259	NSA2	cis	Heart Left Ventricle	GTEx
rs16872259	NSA2	cis	Whole Blood	GTEx
rs16872259	NSA2	cis	Thyroid	GTEx
rs16872259	NSA2	cis	Nerve Tibial	GTEx
rs16872259	TINP1	cis	normal skin	skin_eQTL
rs16872259	NSA2	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:74063800-74069200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:74064000-74070200	Weak transcription	Aorta	Aorta
3	chr5:74064000-74071000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:74064000-74076000	Weak transcription	Esophagus	oesophagus
5	chr5:74064000-74077200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:74064000-74112400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:74064200-74069000	Weak transcription	Thymus	Thymus
8	chr5:74064200-74070600	Weak transcription	Pancreas	Pancrea
9	chr5:74064200-74073000	Weak transcription	Gastric	stomach
10	chr5:74064200-74073800	Weak transcription	Small Intestine	intestine
11	chr5:74064200-74076000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:74064200-74086000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:74064200-74102000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:74064400-74073800	Weak transcription	Stomach Mucosa	stomach
15	chr5:74064400-74076600	Weak transcription	Rectal Smooth Muscle	rectum
16	chr5:74064400-74079600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:74064400-74086600	Weak transcription	Fetal Heart	heart
18	chr5:74064400-74134600	Weak transcription	Fetal Brain Male	brain
19	chr5:74064600-74074400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:74064600-74079400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:74064600-74079600	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr5:74064800-74070000	Strong transcription	Dnd41	blood
23	chr5:74064800-74070000	Strong transcription	HMEC	breast
24	chr5:74064800-74072400	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:74064800-74074000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr5:74064800-74074400	Strong transcription	Osteobl	bone
27	chr5:74064800-74074600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:74064800-74074600	Strong transcription	Primary T helper cells PMA-I stimulated	--
29	chr5:74064800-74074600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:74064800-74074800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr5:74064800-74074800	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr5:74064800-74075000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr5:74064800-74075000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr5:74064800-74075000	Strong transcription	NH-A	brain
35	chr5:74064800-74079400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr5:74064800-74079600	Strong transcription	HUES48 Cell Line	embryonic stem cell
37	chr5:74064800-74080000	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr5:74064800-74080400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr5:74064800-74101200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr5:74065000-74069600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
41	chr5:74065000-74069600	Strong transcription	A549	lung
42	chr5:74065000-74069800	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr5:74065000-74070000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:74065000-74070000	Strong transcription	Duodenum Smooth Muscle	Duodenum
45	chr5:74065000-74070000	Strong transcription	HSMM	muscle
46	chr5:74065000-74070200	Strong transcription	Brain Anterior Caudate	brain
47	chr5:74065000-74070400	Strong transcription	Brain Substantia Nigra	brain
48	chr5:74065000-74070800	Strong transcription	NHDF-Ad	bronchial
49	chr5:74065000-74072000	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr5:74065000-74072000	Strong transcription	Brain Germinal Matrix	brain

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