Variant report

Variant	rs10116142
Chromosome Location	chr9:102727676-102727677
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:102723999..102727062-chr9:102727116..102729040,3	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10117638	0.83[JPT][hapmap]
rs10117828	0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs10120103	0.80[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs10121601	0.94[JPT][hapmap];0.86[YRI][hapmap];0.82[ASN][1000 genomes]
rs10121880	0.80[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs10123261	0.80[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs10124366	0.94[JPT][hapmap]
rs10125981	0.83[JPT][hapmap]
rs10217337	0.93[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs10217366	0.84[ASN][1000 genomes]
rs10217692	0.80[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs10512268	0.80[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs1055187	0.82[JPT][hapmap]
rs10760699	0.83[JPT][hapmap]
rs10760700	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10760704	0.86[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs10760706	0.80[CEU][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs10988920	0.82[ASN][1000 genomes]
rs16918878	0.94[JPT][hapmap]
rs1830454	0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs1852863	0.84[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs1881751	0.81[ASN][1000 genomes]
rs1962051	0.83[JPT][hapmap]
rs1997367	0.80[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs1997368	0.80[CEU][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2031035	0.84[ASN][1000 genomes]
rs2416935	0.80[CEU][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2416936	0.94[JPT][hapmap];0.82[YRI][hapmap]
rs2416937	0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs2416938	0.84[JPT][hapmap]
rs2416940	0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs2416941	0.84[ASN][1000 genomes]
rs2416942	0.84[ASN][1000 genomes]
rs2900224	0.83[ASN][1000 genomes]
rs4282626	0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs4452862	0.80[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs4585797	0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs4742777	0.80[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs4742778	0.80[CEU][hapmap];0.94[JPT][hapmap];0.81[YRI][hapmap];0.84[ASN][1000 genomes]
rs4743370	0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs6478987	0.84[ASN][1000 genomes]
rs6478990	0.84[ASN][1000 genomes]
rs7022208	0.83[JPT][hapmap]
rs7022999	0.84[ASN][1000 genomes]
rs7027619	0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs7027813	0.82[ASN][1000 genomes]
rs7038506	0.94[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs7039716	0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs9299335	0.94[JPT][hapmap];0.82[YRI][hapmap];0.84[ASN][1000 genomes]
rs9556	0.84[CEU][hapmap];0.94[JPT][hapmap];0.85[ASN][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	nsv831668	chr9:102568169-102747293	Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	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
5	nsv1050510	chr9:102684318-102748658	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10116142	STX17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102669800-102729800	Weak transcription	Small Intestine	intestine
2	chr9:102682600-102751400	Weak transcription	NH-A	brain
3	chr9:102685000-102731600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr9:102685200-102730200	Weak transcription	NHLF	lung
5	chr9:102686200-102730000	Weak transcription	Colonic Mucosa	Colon
6	chr9:102686400-102750800	Weak transcription	Esophagus	oesophagus
7	chr9:102686600-102730800	Weak transcription	Ovary	ovary
8	chr9:102686600-102750800	Weak transcription	Gastric	stomach
9	chr9:102698400-102728600	Weak transcription	HMEC	breast
10	chr9:102698400-102728800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:102699800-102739800	Weak transcription	K562	blood
12	chr9:102699800-102765800	Weak transcription	Psoas Muscle	Psoas
13	chr9:102700000-102728600	Weak transcription	A549	lung
14	chr9:102701000-102751000	Weak transcription	Fetal Intestine Small	intestine
15	chr9:102704600-102729200	Weak transcription	Hela-S3	cervix
16	chr9:102705000-102751200	Weak transcription	Brain Angular Gyrus	brain
17	chr9:102708400-102744000	Weak transcription	NHDF-Ad	bronchial
18	chr9:102710600-102729800	Weak transcription	Thymus	Thymus
19	chr9:102711400-102765800	Weak transcription	Right Ventricle	heart
20	chr9:102711400-102769200	Weak transcription	Osteobl	bone
21	chr9:102711800-102749000	Weak transcription	Brain Germinal Matrix	brain
22	chr9:102712000-102728600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr9:102712200-102732400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr9:102712200-102765600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr9:102712400-102729800	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr9:102712400-102751000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr9:102712600-102728600	Weak transcription	NHEK	skin
28	chr9:102712800-102730400	Weak transcription	Lung	lung
29	chr9:102713200-102765600	Weak transcription	HSMMtube	muscle
30	chr9:102713400-102730200	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr9:102714000-102729800	Weak transcription	Left Ventricle	heart
32	chr9:102714200-102749200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr9:102714600-102728400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr9:102714600-102730800	Weak transcription	Dnd41	blood
35	chr9:102715800-102729800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr9:102716000-102728200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:102718000-102777600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr9:102718200-102729800	Weak transcription	GM12878-XiMat	blood
39	chr9:102718400-102731000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr9:102718800-102730800	Weak transcription	Aorta	Aorta
41	chr9:102718800-102751000	Weak transcription	Pancreas	Pancrea
42	chr9:102719000-102739400	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr9:102719000-102765400	Weak transcription	HepG2	liver
44	chr9:102720200-102733200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr9:102720200-102733600	Strong transcription	Liver	Liver
46	chr9:102720200-102736600	Strong transcription	Primary T cells from cord blood	blood
47	chr9:102720400-102732000	Strong transcription	Primary T helper cells PMA-I stimulated	--
48	chr9:102720400-102746400	Weak transcription	Spleen	Spleen
49	chr9:102721600-102739600	Weak transcription	Fetal Brain Female	brain
50	chr9:102721800-102729800	Weak transcription	H1 Cell Line	embryonic stem cell

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