Variant report

Variant	rs9408993
Chromosome Location	chr9:102877633-102877634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:102876067..102878072-chr9:102891854..102894582,2	K562	blood:
2	chr9:102859044..102862948-chr9:102875785..102878003,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000023318	Chromatin interaction
ENSG00000119509	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1014651	0.84[AMR][1000 genomes]
rs10819739	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10988945	0.82[EUR][1000 genomes]
rs10988968	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10988969	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10988973	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10988974	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1099910	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12552646	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1342147	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1361668	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1529191	0.88[EUR][1000 genomes]
rs1535667	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1539297	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1572607	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1578646	0.82[EUR][1000 genomes]
rs1999877	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2057476	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2093696	0.82[EUR][1000 genomes]
rs2181579	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2476439	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2491096	0.81[AMR][1000 genomes]
rs2787364	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2787393	0.82[AMR][1000 genomes]
rs2787396	0.81[AMR][1000 genomes]
rs2806681	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2806684	0.84[AMR][1000 genomes]
rs2806685	0.83[AMR][1000 genomes]
rs2806687	0.81[AMR][1000 genomes]
rs2806688	0.84[AMR][1000 genomes]
rs41346545	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4517187	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4742779	0.82[EUR][1000 genomes]
rs4743379	0.81[EUR][1000 genomes]
rs4743380	0.82[AFR][1000 genomes]
rs4743381	0.83[EUR][1000 genomes]
rs4743382	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4743386	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7018981	0.88[EUR][1000 genomes]
rs7036518	0.88[EUR][1000 genomes]
rs7042194	0.84[EUR][1000 genomes]
rs7047092	0.88[EUR][1000 genomes]
rs7856844	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7858606	0.80[EUR][1000 genomes]
rs7870585	0.82[EUR][1000 genomes]
rs846754	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs846755	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs846759	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs846762	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs846763	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs846766	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs863668	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs942163	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9408993	STX17	cis	Esophagus Mucosa	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102862200-102879800	Weak transcription	Esophagus	oesophagus
2	chr9:102862200-102881000	Weak transcription	Gastric	stomach
3	chr9:102862200-102902400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr9:102862400-102881400	Weak transcription	Colonic Mucosa	Colon
5	chr9:102862800-102881800	Weak transcription	Right Ventricle	heart
6	chr9:102862800-102887400	Weak transcription	Pancreas	Pancrea
7	chr9:102866600-102879000	Weak transcription	Fetal Intestine Small	intestine
8	chr9:102867000-102881000	Weak transcription	Spleen	Spleen
9	chr9:102867000-102899800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:102868600-102895600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr9:102869000-102880200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr9:102869000-102881800	Weak transcription	Psoas Muscle	Psoas
13	chr9:102869000-102886600	Weak transcription	K562	blood
14	chr9:102869000-102888600	Weak transcription	Hela-S3	cervix
15	chr9:102869200-102889800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr9:102869200-102901800	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr9:102869400-102899000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr9:102869800-102895600	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr9:102869800-102896400	Weak transcription	Duodenum Mucosa	Duodenum
20	chr9:102870000-102882800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr9:102870000-102887200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr9:102870000-102892200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr9:102870000-102895800	Weak transcription	Thymus	Thymus
24	chr9:102870000-102902200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:102870200-102881200	Weak transcription	Fetal Kidney	kidney
26	chr9:102870200-102891000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
27	chr9:102870600-102888600	Weak transcription	Fetal Thymus	thymus
28	chr9:102871000-102890200	Weak transcription	HUVEC	blood vessel
29	chr9:102871200-102890600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr9:102871200-102897400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr9:102871400-102890200	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr9:102872000-102896600	Weak transcription	Placenta	Placenta
33	chr9:102872600-102883400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr9:102872800-102879400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr9:102872800-102895000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr9:102873800-102882400	Weak transcription	Primary B cells from cord blood	blood
37	chr9:102873800-102888400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr9:102873800-102895800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr9:102873800-102900200	Weak transcription	Primary T cells fromperipheralblood	blood
40	chr9:102874000-102879200	Weak transcription	Ovary	ovary
41	chr9:102874000-102884400	Weak transcription	GM12878-XiMat	blood
42	chr9:102874000-102888600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr9:102874000-102896000	Weak transcription	Colon Smooth Muscle	Colon
44	chr9:102874000-102896000	Weak transcription	Lung	lung
45	chr9:102874200-102878400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr9:102874200-102879200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr9:102874200-102879200	Weak transcription	Adipose Nuclei	Adipose
48	chr9:102874200-102879800	Weak transcription	HSMM	muscle
49	chr9:102874200-102880400	Weak transcription	NHLF	lung
50	chr9:102874200-102881800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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