Variant report

Variant	rs10988934
Chromosome Location	chr9:102752686-102752687
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10760711	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10819714	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10819715	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10988945	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10988968	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10988969	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12685650	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1342147	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1361668	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1529191	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1578646	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2057476	0.80[EUR][1000 genomes]
rs2093696	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2209082	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2698999	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2791335	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2791336	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2791337	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2795575	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35493819	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs41346545	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4517187	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4742779	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4743379	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4743380	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4743381	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4743382	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7018981	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7036518	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7042194	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7047092	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7858606	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7862460	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7870585	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7874449	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs846754	0.80[EUR][1000 genomes]
rs942163	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[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
rs10988934	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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