Variant report

Variant	rs890897
Chromosome Location	chr16:12662587-12662588
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10609	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs1061008	0.80[YRI][hapmap]
rs1075842	0.84[AFR][1000 genomes]
rs11075096	0.81[CHB][hapmap];0.84[CHD][hapmap]
rs11639949	0.91[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs11640384	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs11643626	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11643633	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs11644936	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs12162086	0.90[CHB][hapmap]
rs12477	0.81[EUR][1000 genomes]
rs12918863	0.80[AFR][1000 genomes]
rs12918996	0.80[AFR][1000 genomes]
rs12924625	0.94[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.86[LWK][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap]
rs12925894	0.82[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.88[TSI][hapmap]
rs12925945	0.94[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap]
rs12926426	0.90[CHB][hapmap]
rs12927563	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap]
rs12928426	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12928849	0.91[CHB][hapmap];0.91[CHD][hapmap];0.82[TSI][hapmap]
rs12929849	0.84[CEU][hapmap];0.95[CHB][hapmap]
rs12930375	0.89[ASW][hapmap];0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.89[LWK][hapmap];0.87[TSI][hapmap];0.96[YRI][hapmap]
rs12931667	0.86[CHB][hapmap]
rs12935425	0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[YRI][hapmap]
rs1560114	0.80[YRI][hapmap]
rs2081896	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs2162794	0.90[CHB][hapmap]
rs2288422	0.81[EUR][1000 genomes]
rs2288423	0.81[EUR][1000 genomes]
rs3169265	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs3169266	0.81[EUR][1000 genomes]
rs3169267	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.80[EUR][1000 genomes]
rs34352915	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs35804561	0.80[AFR][1000 genomes]
rs36121403	0.80[AFR][1000 genomes]
rs3751783	0.91[CHB][hapmap]
rs3751785	0.91[CHB][hapmap]
rs3803604	0.95[CEU][hapmap];0.86[TSI][hapmap]
rs3803605	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap]
rs3803607	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs3803610	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes]
rs3803614	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs3826099	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs3826100	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs3826101	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs3826102	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap]
rs3826105	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap]
rs3829530	0.86[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs4287557	0.90[CHB][hapmap]
rs5018323	0.89[ASW][hapmap];0.82[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.89[LWK][hapmap];0.81[MEX][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap]
rs60215082	0.83[AFR][1000 genomes]
rs7200321	0.91[CHB][hapmap]
rs7201769	0.91[CHB][hapmap];0.93[CHD][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs7205432	0.91[CHB][hapmap];0.95[CHD][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap]
rs745829	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap]
rs7619	0.81[EUR][1000 genomes]
rs7620	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs890896	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1051242	chr16:12482972-12897243	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv542749	chr16:12482972-12897243	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer 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 miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1035581	chr16:12516946-12863700	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1051607	chr16:12522130-13347676	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv542750	chr16:12522130-13347676	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	esv1842867	chr16:12632286-12678721	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	esv2751546	chr16:12635498-12674704	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv1050925	chr16:12648058-12670588	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv1044772	chr16:12648266-12668751	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1049011	chr16:12655176-12672143	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv9349	chr16:12656022-12674639	Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs890897	SHISA9	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12613000-12670800	Weak transcription	Pancreas	Pancrea
2	chr16:12632800-12663800	Weak transcription	Aorta	Aorta
3	chr16:12641200-12667000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr16:12647400-12665200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr16:12648400-12668800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr16:12652200-12669200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr16:12652400-12666400	Weak transcription	Brain Anterior Caudate	brain
8	chr16:12652600-12665800	Weak transcription	Brain Angular Gyrus	brain
9	chr16:12652600-12672200	Weak transcription	Right Ventricle	heart
10	chr16:12652800-12663400	Weak transcription	Brain Substantia Nigra	brain
11	chr16:12653200-12667600	Weak transcription	Brain Hippocampus Middle	brain
12	chr16:12653200-12669200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr16:12653600-12662600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr16:12653600-12663200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr16:12653800-12662600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr16:12653800-12665800	Weak transcription	NHDF-Ad	bronchial
17	chr16:12656400-12664200	Weak transcription	Left Ventricle	heart
18	chr16:12657600-12664400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr16:12659600-12663200	Weak transcription	Placenta	Placenta
20	chr16:12659600-12664000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr16:12659600-12666000	Strong transcription	Primary B cells from peripheral blood	blood
22	chr16:12659800-12663400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr16:12660000-12666200	Weak transcription	Fetal Muscle Trunk	muscle
24	chr16:12660200-12663000	Weak transcription	GM12878-XiMat	blood
25	chr16:12660200-12663400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr16:12660400-12664000	Weak transcription	Fetal Intestine Small	intestine
27	chr16:12660600-12664600	Strong transcription	Adipose Nuclei	Adipose
28	chr16:12660600-12666600	Strong transcription	Primary B cells from cord blood	blood
29	chr16:12660800-12666400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr16:12661000-12664000	Weak transcription	HepG2	liver
31	chr16:12661000-12664800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr16:12661200-12667000	Weak transcription	Fetal Lung	lung
33	chr16:12661200-12667400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr16:12661400-12662600	Weak transcription	Ovary	ovary
35	chr16:12661400-12668200	Weak transcription	Duodenum Mucosa	Duodenum
36	chr16:12661600-12663200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr16:12661600-12663400	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr16:12661600-12664400	ZNF genes & repeats	Lung	lung
39	chr16:12661600-12665000	Strong transcription	Spleen	Spleen
40	chr16:12661800-12663400	Weak transcription	Primary T cells from cord blood	blood
41	chr16:12661800-12667200	Weak transcription	HSMMtube	muscle
42	chr16:12661800-12667600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr16:12661800-12670400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr16:12662000-12663200	Weak transcription	Fetal Thymus	thymus
45	chr16:12662000-12665400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr16:12662000-12667400	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr16:12662000-12667400	Weak transcription	Primary hematopoietic stem cells	blood
48	chr16:12662000-12667600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr16:12662200-12662800	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr16:12662200-12662800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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