Variant report

Variant	rs17345786
Chromosome Location	chr3:101318318-101318319
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZBTB11-1	chr3:101318087-101318488	NONHSAT090894

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1031710	0.90[JPT][hapmap]
rs10936707	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11707250	0.85[JPT][hapmap];0.84[LWK][hapmap]
rs11708616	0.90[CEU][hapmap];0.80[JPT][hapmap]
rs11708845	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11710016	0.91[CEU][hapmap];0.89[GIH][hapmap];0.83[TSI][hapmap]
rs11710533	0.85[ASN][1000 genomes]
rs11711808	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs11711903	0.80[JPT][hapmap]
rs11712748	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs11714444	0.85[JPT][hapmap]
rs11715368	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11717638	0.85[JPT][hapmap]
rs11720560	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11914318	0.95[JPT][hapmap]
rs11917569	0.84[ASN][1000 genomes]
rs11917682	0.84[ASN][1000 genomes]
rs11919389	0.90[JPT][hapmap]
rs11923273	0.88[ASN][1000 genomes]
rs12629658	0.84[ASN][1000 genomes]
rs12639028	0.87[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]
rs13085776	0.85[JPT][hapmap]
rs1460097	0.85[JPT][hapmap]
rs1609159	0.93[MKK][hapmap]
rs17345528	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17347156	0.80[JPT][hapmap]
rs17411983	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs17508319	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288272	0.83[GIH][hapmap];0.95[JPT][hapmap];0.86[LWK][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	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804775	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3804778	1.00[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];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3806653	0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap]
rs3806654	0.95[JPT][hapmap]
rs4257518	0.95[MKK][hapmap];0.90[YRI][hapmap]
rs4342086	0.80[JPT][hapmap];0.84[LWK][hapmap]
rs55641278	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs58835747	0.81[EUR][1000 genomes]
rs58907984	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60837174	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6791964	0.86[EUR][1000 genomes]
rs72946021	0.85[EUR][1000 genomes]
rs73863360	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629753	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs7641261	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7651721	0.83[GIH][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap]
rs9830943	0.90[JPT][hapmap]
rs997739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv963347	chr3:101318121-101342898	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17345786	NIT2	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101294200-101319400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:101296000-101324600	Weak transcription	Aorta	Aorta
3	chr3:101302600-101319600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:101304200-101319600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr3:101305800-101319800	Weak transcription	Pancreas	Pancrea
6	chr3:101305800-101322600	Weak transcription	HSMMtube	muscle
7	chr3:101305800-101324400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr3:101309600-101320200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:101309600-101324000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:101310000-101319800	Weak transcription	Right Ventricle	heart
11	chr3:101310000-101320400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr3:101310200-101320000	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:101310400-101320000	Weak transcription	Primary T cells from cord blood	blood
14	chr3:101310400-101320000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:101310400-101320200	Weak transcription	Brain Germinal Matrix	brain
16	chr3:101310400-101322400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr3:101310400-101324800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:101310800-101320000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:101311000-101319800	Weak transcription	NHLF	lung
20	chr3:101311000-101321000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:101311000-101329800	Weak transcription	Thymus	Thymus
22	chr3:101311400-101319800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr3:101311400-101324400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr3:101311400-101324600	Weak transcription	Esophagus	oesophagus
25	chr3:101311400-101329600	Weak transcription	K562	blood
26	chr3:101312200-101319000	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr3:101312800-101321400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr3:101313000-101321000	Weak transcription	HMEC	breast
29	chr3:101313200-101322200	Weak transcription	Placenta	Placenta
30	chr3:101313400-101321400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr3:101313400-101324600	Weak transcription	HSMM	muscle
32	chr3:101313800-101320000	Weak transcription	Osteobl	bone
33	chr3:101314400-101320000	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr3:101314400-101320000	Weak transcription	Fetal Brain Female	brain
35	chr3:101314400-101321000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:101314400-101324000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:101314800-101321400	Weak transcription	Fetal Intestine Small	intestine
38	chr3:101314800-101328200	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr3:101315000-101319800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr3:101315000-101320000	Weak transcription	Liver	Liver
41	chr3:101315000-101320800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:101315000-101321000	Weak transcription	NHEK	skin
43	chr3:101315000-101321200	Weak transcription	Left Ventricle	heart
44	chr3:101315000-101321200	Weak transcription	GM12878-XiMat	blood
45	chr3:101315000-101321600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:101315000-101323200	Weak transcription	Lung	lung
47	chr3:101315200-101321400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:101315200-101321400	Weak transcription	NH-A	brain
49	chr3:101315400-101319800	Weak transcription	Dnd41	blood
50	chr3:101316000-101318600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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