Variant report

Variant	rs12708747
Chromosome Location	chr16:12218559-12218560
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	GATA2	chr16:12218466-12218827	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
SNX29	TF binding region

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs11075049	0.82[JPT][hapmap]
rs11075054	0.95[ASN][1000 genomes]
rs11642033	0.91[ASN][1000 genomes]
rs11642386	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs11646458	0.86[ASN][1000 genomes]
rs11646539	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11646584	0.91[ASN][1000 genomes]
rs11647572	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11648468	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs11648816	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12596703	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12599107	0.90[ASN][1000 genomes]
rs12599793	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12924889	0.91[ASN][1000 genomes]
rs12926900	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12929519	0.91[ASN][1000 genomes]
rs13333662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13336687	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs16958964	0.90[CHB][hapmap];0.87[JPT][hapmap]
rs2136250	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2175020	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[ASN][1000 genomes]
rs34098770	0.89[ASN][1000 genomes]
rs34147612	0.81[ASN][1000 genomes]
rs34598762	0.81[ASN][1000 genomes]
rs35293822	0.97[ASN][1000 genomes]
rs35542345	0.91[ASN][1000 genomes]
rs3851011	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs3851012	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs3851013	1.00[ASN][1000 genomes]
rs3851014	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3862466	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3893358	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4781180	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs8048589	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs8050180	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs8063329	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs9925009	0.82[CHB][hapmap]
rs9935284	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9936270	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9939383	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905347	chr16:12010444-12243329	Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	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
3	nsv1043959	chr16:12039346-12285269	Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	nsv977111	chr16:12161129-12220593	Weak transcription Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv571460	chr16:12181702-12238602	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1052973	chr16:12188092-12307880	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1042146	chr16:12208242-12256699	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12708747	SHISA9	cis	parietal	SCAN

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12184400-12231200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr16:12189800-12220400	Weak transcription	Primary T helper cells fromperipheralblood	blood
3	chr16:12190000-12220200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr16:12190000-12220400	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr16:12191200-12223200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr16:12198200-12227800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr16:12200200-12220200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr16:12204800-12222000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr16:12208000-12221200	Weak transcription	Brain Substantia Nigra	brain
10	chr16:12208200-12228000	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr16:12208400-12218800	Weak transcription	Brain Anterior Caudate	brain
12	chr16:12208600-12226800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr16:12211000-12218600	Weak transcription	Thymus	Thymus
14	chr16:12211000-12218600	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr16:12211000-12224400	Weak transcription	Duodenum Mucosa	Duodenum
16	chr16:12211000-12227800	Weak transcription	Fetal Intestine Small	intestine
17	chr16:12211200-12221400	Weak transcription	GM12878-XiMat	blood
18	chr16:12211200-12223200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr16:12211200-12223400	Weak transcription	Aorta	Aorta
20	chr16:12211200-12224400	Weak transcription	Pancreas	Pancrea
21	chr16:12211200-12226200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr16:12213000-12221400	Weak transcription	Primary T cells from cord blood	blood
23	chr16:12213200-12232600	Weak transcription	Colonic Mucosa	Colon
24	chr16:12213800-12226600	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr16:12213800-12228200	Weak transcription	Lung	lung
26	chr16:12213800-12228400	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr16:12213800-12231400	Weak transcription	Small Intestine	intestine
28	chr16:12213800-12255400	Weak transcription	Gastric	stomach
29	chr16:12214000-12221600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr16:12214000-12221600	Weak transcription	Adipose Nuclei	Adipose
31	chr16:12214000-12226400	Weak transcription	HSMM	muscle
32	chr16:12214000-12228000	Weak transcription	Brain Cingulate Gyrus	brain
33	chr16:12214200-12221200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr16:12214400-12224600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr16:12214600-12220000	Weak transcription	HMEC	breast
36	chr16:12214600-12224200	Weak transcription	Brain Angular Gyrus	brain
37	chr16:12214800-12221600	Weak transcription	HSMMtube	muscle
38	chr16:12215000-12218600	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr16:12215000-12218600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr16:12215000-12219600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr16:12215000-12219600	Weak transcription	NHEK	skin
42	chr16:12215000-12226800	Weak transcription	Ovary	ovary
43	chr16:12215000-12227600	Weak transcription	Stomach Smooth Muscle	stomach
44	chr16:12215000-12227800	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr16:12215000-12228200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr16:12215000-12233200	Weak transcription	Fetal Lung	lung
47	chr16:12215200-12218800	Weak transcription	Fetal Kidney	kidney
48	chr16:12215200-12221400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr16:12215200-12221400	Weak transcription	Right Atrium	heart
50	chr16:12215200-12221600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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