Variant report

Variant	rs9165
Chromosome Location	chr12:122219787-122219788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11837955	0.80[AFR][1000 genomes]
rs12310051	0.82[AFR][1000 genomes]
rs12318048	0.82[AFR][1000 genomes]
rs2242259	0.87[JPT][hapmap]
rs2242260	0.87[JPT][hapmap]
rs28493021	0.82[AFR][1000 genomes]
rs34415086	0.82[AFR][1000 genomes]
rs3741593	0.81[JPT][hapmap]
rs7136373	0.93[LWK][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes]
rs73413728	0.82[AFR][1000 genomes]
rs9282	0.87[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
3	nsv899567	chr12:122203680-122281575	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9165	SRSF9	cis	parietal	SCAN
rs9165	CCDC62	cis	parietal	SCAN
rs9165	FBXW8	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122183800-122224400	Weak transcription	Small Intestine	intestine
2	chr12:122206400-122228200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr12:122206400-122230600	Weak transcription	Brain Angular Gyrus	brain
4	chr12:122206600-122220000	Weak transcription	Brain Anterior Caudate	brain
5	chr12:122206600-122226400	Weak transcription	Aorta	Aorta
6	chr12:122211600-122225000	Weak transcription	Psoas Muscle	Psoas
7	chr12:122211600-122231200	Weak transcription	Brain Hippocampus Middle	brain
8	chr12:122211800-122219800	Weak transcription	Fetal Lung	lung
9	chr12:122211800-122231600	Weak transcription	Brain Substantia Nigra	brain
10	chr12:122213400-122221200	Genic enhancers	Fetal Thymus	thymus
11	chr12:122214200-122219800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:122214200-122228200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:122214400-122220400	Weak transcription	Right Atrium	heart
14	chr12:122214600-122220200	Weak transcription	Stomach Mucosa	stomach
15	chr12:122214600-122224200	Weak transcription	Pancreas	Pancrea
16	chr12:122214600-122224800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:122215400-122223000	Genic enhancers	Primary T cells fromperipheralblood	blood
18	chr12:122217200-122222400	Weak transcription	Liver	Liver
19	chr12:122217600-122219800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:122217600-122220000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
21	chr12:122217800-122230400	Weak transcription	Brain Cingulate Gyrus	brain
22	chr12:122218600-122219800	Genic enhancers	Primary B cells from cord blood	blood
23	chr12:122218600-122220000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr12:122218600-122220600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr12:122218800-122219800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:122218800-122219800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr12:122218800-122220000	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr12:122218800-122220000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr12:122218800-122220600	Enhancers	Esophagus	oesophagus
30	chr12:122218800-122220600	Genic enhancers	Spleen	Spleen
31	chr12:122218800-122220800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr12:122218800-122221200	Enhancers	Primary hematopoietic stem cells	blood
33	chr12:122219000-122220000	Genic enhancers	Primary T cells from cord blood	blood
34	chr12:122219000-122220000	Enhancers	Muscle Satellite Cultured Cells	--
35	chr12:122219000-122220600	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr12:122219000-122220800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr12:122219000-122220800	Genic enhancers	Fetal Muscle Leg	muscle
38	chr12:122219000-122220800	Enhancers	NH-A	brain
39	chr12:122219000-122221000	Enhancers	Fetal Muscle Trunk	muscle
40	chr12:122219000-122225000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:122219000-122227400	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr12:122219000-122229800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:122219200-122219800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr12:122219200-122219800	Enhancers	Colon Smooth Muscle	Colon
45	chr12:122219200-122220200	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr12:122219200-122220400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:122219200-122220600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr12:122219200-122220600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
49	chr12:122219200-122220800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:122219200-122220800	Enhancers	NHEK	skin

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