Variant report

Variant	rs17345528
Chromosome Location	chr3:101294830-101294831
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:101293909..101295477-chr3:101345124..101347411,2	K562	blood:
2	chr3:101294680..101296540-chr3:101306521..101308762,3	MCF-7	breast:
3	chr3:101289369..101294999-chr3:101391357..101396813,8	K562	blood:
4	chr3:101291104..101295547-chr3:101393750..101397705,12	MCF-7	breast:
5	chr3:101293308..101296113-chr3:101394030..101397396,3	MCF-7	breast:
6	chr3:101290641..101295184-chr3:101404268..101406806,5	MCF-7	breast:
7	chr3:101291201..101295304-chr3:101402286..101407928,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000081154	Chromatin interaction
ENSG00000212319	Chromatin interaction
ENSG00000114391	Chromatin interaction
ENSG00000066422	Chromatin interaction
ENSG00000256628	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1031710	0.90[JPT][hapmap]
rs10936707	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11708616	0.85[CEU][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs11708845	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11710016	0.86[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap]
rs11710533	0.81[ASN][1000 genomes]
rs11711808	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs11712748	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs11715368	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11720560	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11914318	0.95[JPT][hapmap]
rs11919389	0.90[JPT][hapmap]
rs11923273	0.84[ASN][1000 genomes]
rs12638137	0.81[EUR][1000 genomes]
rs12638796	0.85[EUR][1000 genomes]
rs12639028	0.82[ASN][1000 genomes]
rs13059470	0.83[GIH][hapmap];0.90[JPT][hapmap]
rs13065944	0.90[JPT][hapmap]
rs13066768	0.90[JPT][hapmap]
rs13069443	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs13081846	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs1609159	0.95[MKK][hapmap];0.85[YRI][hapmap]
rs17345786	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17411983	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs17508319	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288272	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs3094296	0.95[JPT][hapmap]
rs3094297	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs34376498	0.90[JPT][hapmap]
rs35117343	0.90[JPT][hapmap]
rs35850993	0.90[JPT][hapmap]
rs3762729	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3804775	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3804778	0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3806653	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs3806654	0.95[JPT][hapmap]
rs4257518	0.93[MKK][hapmap]
rs55641278	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55710435	0.85[EUR][1000 genomes]
rs57880921	0.85[EUR][1000 genomes]
rs58835747	0.88[EUR][1000 genomes]
rs58907984	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59359251	0.81[EUR][1000 genomes]
rs60837174	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6791964	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72944107	0.85[EUR][1000 genomes]
rs72946021	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73863360	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7629753	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs7641261	0.95[CEU][hapmap];0.84[CHB][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7651721	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs9830943	0.90[JPT][hapmap]
rs997739	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17345528	NIT2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101291600-101295000	Active TSS	K562	blood
2	chr3:101292000-101295000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr3:101292000-101295200	Active TSS	Psoas Muscle	Psoas
4	chr3:101292200-101295000	Active TSS	Right Atrium	heart
5	chr3:101292400-101295000	Active TSS	Breast Myoepithelial Primary Cells	Breast
6	chr3:101292400-101295000	Active TSS	HSMMtube	muscle
7	chr3:101292600-101295000	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr3:101292600-101295000	Active TSS	A549	lung
9	chr3:101292600-101295000	Active TSS	NH-A	brain
10	chr3:101292600-101295200	Active TSS	HMEC	breast
11	chr3:101293600-101295000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:101293800-101295000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:101293800-101295000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr3:101293800-101295600	Weak transcription	Spleen	Spleen
15	chr3:101294000-101295000	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr3:101294000-101295000	Flanking Active TSS	HUVEC	blood vessel
17	chr3:101294000-101295000	Flanking Active TSS	Osteobl	bone
18	chr3:101294000-101295200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr3:101294000-101295200	Weak transcription	Ovary	ovary
20	chr3:101294000-101295600	Weak transcription	Gastric	stomach
21	chr3:101294000-101295600	Weak transcription	Left Ventricle	heart
22	chr3:101294000-101295600	Weak transcription	Lung	lung
23	chr3:101294000-101295600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:101294000-101298400	Weak transcription	Pancreas	Pancrea
25	chr3:101294000-101298400	Weak transcription	Small Intestine	intestine
26	chr3:101294000-101301800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:101294000-101305200	Weak transcription	Esophagus	oesophagus
28	chr3:101294000-101312200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:101294200-101295000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:101294200-101295000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr3:101294200-101295000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr3:101294200-101295000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr3:101294200-101295000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr3:101294200-101295000	Enhancers	Adipose Nuclei	Adipose
35	chr3:101294200-101295000	Enhancers	Brain Angular Gyrus	brain
36	chr3:101294200-101295000	Enhancers	Brain Hippocampus Middle	brain
37	chr3:101294200-101295200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:101294200-101295600	Enhancers	Primary T cells fromperipheralblood	blood
39	chr3:101294200-101295600	Weak transcription	Aorta	Aorta
40	chr3:101294200-101295600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr3:101294200-101296000	Weak transcription	Placenta	Placenta
42	chr3:101294200-101309000	Weak transcription	Colonic Mucosa	Colon
43	chr3:101294200-101310000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr3:101294200-101319400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr3:101294400-101295000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:101294400-101295000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr3:101294400-101295000	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr3:101294400-101295000	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr3:101294400-101295000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr3:101294400-101295000	Enhancers	Fetal Stomach	stomach

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