Variant report

Variant	rs2787390
Chromosome Location	chr9:103013986-103013987
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10117799	0.87[ASN][1000 genomes]
rs10118701	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs10123866	0.87[ASN][1000 genomes]
rs10123913	0.87[ASN][1000 genomes]
rs10124893	0.88[ASN][1000 genomes]
rs10125785	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1014652	0.83[CHD][hapmap]
rs10739795	0.83[CHD][hapmap]
rs10760724	0.85[ASN][1000 genomes]
rs10819751	0.91[ASN][1000 genomes]
rs10819759	0.85[CHB][hapmap];1.00[CHD][hapmap];0.83[ASN][1000 genomes]
rs10988973	0.83[CHD][hapmap]
rs10989049	0.88[ASN][1000 genomes]
rs10989064	0.85[CHB][hapmap];1.00[CHD][hapmap]
rs10989067	0.85[CHB][hapmap]
rs11789196	0.87[ASN][1000 genomes]
rs12552646	0.83[CHD][hapmap]
rs1338121	1.00[CHD][hapmap]
rs1338123	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1338124	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs1338125	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs1342147	0.83[CHD][hapmap]
rs1529191	0.83[CHD][hapmap]
rs1529192	0.83[CHD][hapmap]
rs1572607	0.83[CHD][hapmap]
rs1930243	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs1930244	0.85[ASN][1000 genomes]
rs1999877	0.83[CHD][hapmap]
rs2065997	1.00[CHD][hapmap]
rs2151131	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[ASN][1000 genomes]
rs2181579	0.83[CHD][hapmap]
rs2245216	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2476441	0.83[CHD][hapmap]
rs2485745	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs2787361	0.83[CHD][hapmap]
rs2787364	0.83[CHD][hapmap]
rs2787365	0.83[CHD][hapmap]
rs2787366	0.83[CHD][hapmap]
rs2787368	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs2787369	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs2787370	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2787371	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2787372	0.85[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs2787373	0.90[ASN][1000 genomes]
rs2787374	1.00[CHD][hapmap]
rs2787375	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs2787376	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2787377	0.88[ASN][1000 genomes]
rs2787380	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2787381	0.90[ASN][1000 genomes]
rs2787383	0.91[ASN][1000 genomes]
rs2787385	0.90[ASN][1000 genomes]
rs2787388	0.91[ASN][1000 genomes]
rs2787395	0.83[CHD][hapmap]
rs2787397	0.91[CHD][hapmap]
rs2806681	0.83[CHD][hapmap]
rs2806687	0.83[CHD][hapmap]
rs2806691	1.00[CHD][hapmap]
rs2806692	0.91[ASN][1000 genomes]
rs2806693	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs2806694	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs2806695	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2806696	1.00[CHB][hapmap];0.91[ASN][1000 genomes]
rs2806699	1.00[CHD][hapmap]
rs2806700	1.00[CHB][hapmap];0.92[CHD][hapmap]
rs2806702	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs2806703	0.85[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs3813712	1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[ASN][1000 genomes]
rs3923501	0.88[ASN][1000 genomes]
rs4128230	0.85[ASN][1000 genomes]
rs4237194	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4237195	0.85[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs4446782	0.88[ASN][1000 genomes]
rs4517187	0.83[CHD][hapmap]
rs4742782	0.87[ASN][1000 genomes]
rs4742783	0.81[ASN][1000 genomes]
rs4742784	0.85[CHB][hapmap]
rs4743392	0.88[ASN][1000 genomes]
rs4743393	0.85[CHB][hapmap];0.83[ASN][1000 genomes]
rs4743395	0.85[CHB][hapmap]
rs5029342	0.87[ASN][1000 genomes]
rs5029343	0.88[ASN][1000 genomes]
rs6479001	0.83[CHD][hapmap]
rs6479002	0.83[CHD][hapmap]
rs6479008	0.83[ASN][1000 genomes]
rs6479009	0.88[ASN][1000 genomes]
rs6479013	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs6479014	1.00[CHB][hapmap]
rs7020988	0.88[ASN][1000 genomes]
rs7025938	0.85[CHD][hapmap];0.87[ASN][1000 genomes]
rs7035619	0.85[CHB][hapmap];0.87[ASN][1000 genomes]
rs7048601	1.00[CHB][hapmap];0.84[ASN][1000 genomes]
rs7472	0.87[ASN][1000 genomes]
rs7846794	0.83[CHD][hapmap]
rs7849966	0.88[ASN][1000 genomes]
rs7854693	0.87[ASN][1000 genomes]
rs7861003	0.83[CHD][hapmap]
rs7864494	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[ASN][1000 genomes]
rs7874900	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs846753	0.83[CHD][hapmap]
rs846756	0.83[CHD][hapmap]
rs846766	0.83[CHD][hapmap]
rs914711	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs9408998	0.81[ASN][1000 genomes]
rs944710	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs946054	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs959893	0.81[ASN][1000 genomes]
rs9775014	0.82[ASN][1000 genomes]
rs9775182	0.88[ASN][1000 genomes]
rs9886877	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529618	chr9:102227922-103044018	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv531599	chr9:102227922-103156864	Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv1048674	chr9:102752236-103038259	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1052007	chr9:102766948-103033937	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	esv1835721	chr9:102991314-103096666	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2787390	HSD17B3	cis	cerebellum	SCAN
rs2787390	TEX10	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102958800-103014400	Weak transcription	Hela-S3	cervix
2	chr9:102972400-103017200	Weak transcription	Spleen	Spleen
3	chr9:102972400-103035200	Weak transcription	Esophagus	oesophagus
4	chr9:102972600-103027200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr9:102972600-103046600	Weak transcription	Psoas Muscle	Psoas
6	chr9:102973000-103014600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr9:102973000-103027400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr9:102973000-103053800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr9:102974000-103014000	Weak transcription	Brain Substantia Nigra	brain
10	chr9:102974000-103014600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:102974000-103047600	Weak transcription	Fetal Brain Male	brain
12	chr9:102974200-103014600	Weak transcription	Brain Angular Gyrus	brain
13	chr9:102975800-103045800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr9:102976800-103047800	Weak transcription	Fetal Heart	heart
15	chr9:102977000-103014600	Weak transcription	NH-A	brain
16	chr9:102979400-103054600	Weak transcription	NHEK	skin
17	chr9:102984000-103014600	Weak transcription	HSMMtube	muscle
18	chr9:102985800-103014400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr9:102986600-103018800	Weak transcription	Small Intestine	intestine
20	chr9:102987400-103014600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr9:102987400-103045800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:102987400-103054600	Weak transcription	Gastric	stomach
23	chr9:102989400-103014600	Weak transcription	Brain Hippocampus Middle	brain
24	chr9:102989400-103047200	Weak transcription	GM12878-XiMat	blood
25	chr9:102989600-103014400	Weak transcription	Osteobl	bone
26	chr9:102989600-103027600	Weak transcription	A549	lung
27	chr9:102989800-103014600	Weak transcription	Placenta	Placenta
28	chr9:102990200-103014600	Weak transcription	Brain Anterior Caudate	brain
29	chr9:102991000-103016600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr9:102991400-103014400	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr9:102992400-103014600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr9:102992400-103027200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr9:102992600-103039000	Weak transcription	NHDF-Ad	bronchial
34	chr9:102994800-103046600	Weak transcription	Pancreas	Pancrea
35	chr9:102995000-103014400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr9:102997800-103054400	Weak transcription	Colonic Mucosa	Colon
37	chr9:102999600-103014000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr9:102999600-103027400	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr9:102999800-103014600	Weak transcription	Thymus	Thymus
40	chr9:102999800-103020600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr9:102999800-103028000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr9:102999800-103035200	Weak transcription	Right Ventricle	heart
43	chr9:103000000-103014600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr9:103000000-103014600	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr9:103000000-103021000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr9:103000000-103021000	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr9:103000000-103021000	Weak transcription	Fetal Thymus	thymus
48	chr9:103000000-103021000	Weak transcription	Lung	lung
49	chr9:103000000-103021600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr9:103000000-103034800	Weak transcription	Aorta	Aorta

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