Variant report

Variant	rs6478992
Chromosome Location	chr9:102753959-102753960
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10739795	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10760710	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10760712	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10819716	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10819717	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10819719	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10988963	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11555502	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1406613	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1418267	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1529192	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1529193	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1534726	0.82[EUR][1000 genomes]
rs1578644	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1578645	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1852864	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1852865	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1891334	0.82[EUR][1000 genomes]
rs2096158	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2104273	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2416985	0.81[AMR][1000 genomes]
rs28448789	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4495492	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4503155	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4743375	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4743376	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4743384	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6478991	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6478994	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6478995	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6478996	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6478997	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6478998	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6479000	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6479001	0.82[EUR][1000 genomes]
rs6479002	0.82[EUR][1000 genomes]
rs7022493	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7024016	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7025300	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7026532	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7027414	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7029020	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7029048	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7032333	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7033091	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7037362	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7041338	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7042912	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7043057	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7044219	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7853485	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7857530	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6478992	STX17	cis	Esophagus Mucosa	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102699800-102765800	Weak transcription	Psoas Muscle	Psoas
2	chr9:102711400-102765800	Weak transcription	Right Ventricle	heart
3	chr9:102711400-102769200	Weak transcription	Osteobl	bone
4	chr9:102712200-102765600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr9:102713200-102765600	Weak transcription	HSMMtube	muscle
6	chr9:102718000-102777600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr9:102719000-102765400	Weak transcription	HepG2	liver
8	chr9:102729400-102764600	Weak transcription	HSMM	muscle
9	chr9:102729600-102765600	Weak transcription	NHEK	skin
10	chr9:102729600-102826800	Weak transcription	HMEC	breast
11	chr9:102730200-102765600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr9:102731000-102765600	Weak transcription	NHLF	lung
13	chr9:102731000-102778200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr9:102731800-102765600	Weak transcription	Small Intestine	intestine
15	chr9:102732600-102765600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr9:102733000-102765600	Weak transcription	Colon Smooth Muscle	Colon
17	chr9:102733200-102765000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr9:102735800-102764600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr9:102740600-102765600	Weak transcription	A549	lung
20	chr9:102740800-102765400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:102740800-102765600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr9:102743400-102765600	Weak transcription	K562	blood
23	chr9:102744800-102765600	Weak transcription	NHDF-Ad	bronchial
24	chr9:102745200-102765600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:102745400-102765200	Weak transcription	Hela-S3	cervix
26	chr9:102746200-102765000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr9:102747000-102765400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr9:102747600-102765600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr9:102748000-102756400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr9:102748200-102758200	Weak transcription	Monocytes-CD14+_RO01746	blood
31	chr9:102749400-102764600	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr9:102749400-102765600	Weak transcription	Brain Hippocampus Middle	brain
33	chr9:102751200-102759800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr9:102751400-102756400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr9:102751400-102760600	Weak transcription	Lung	lung
36	chr9:102751400-102763400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr9:102751400-102765600	Weak transcription	Aorta	Aorta
38	chr9:102751400-102765600	Weak transcription	Left Ventricle	heart
39	chr9:102751600-102757800	Weak transcription	Liver	Liver
40	chr9:102751600-102760400	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr9:102751600-102765600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr9:102751600-102765600	Weak transcription	Esophagus	oesophagus
43	chr9:102751600-102765600	Weak transcription	Fetal Thymus	thymus
44	chr9:102751600-102765600	Weak transcription	Gastric	stomach
45	chr9:102751600-102765600	Weak transcription	Dnd41	blood
46	chr9:102751600-102765800	Weak transcription	Colonic Mucosa	Colon
47	chr9:102751800-102760000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:102751800-102760600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr9:102751800-102760600	Weak transcription	Pancreas	Pancrea
50	chr9:102751800-102760600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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