Variant report

Variant	rs9556
Chromosome Location	chr9:102732237-102732238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10116142	0.84[CEU][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs10117638	0.82[CHD][hapmap]
rs10117828	0.96[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10118565	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10120103	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10121601	0.96[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10121880	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10123261	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10124366	0.81[CHD][hapmap];0.87[JPT][hapmap]
rs10217337	0.95[CEU][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10217366	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10217692	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10512268	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1055187	0.89[CHB][hapmap];0.95[CHD][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs10760699	0.82[CHD][hapmap]
rs10760700	0.92[CEU][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10760704	1.00[CEU][hapmap];0.95[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10760706	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10988920	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10988945	0.83[YRI][hapmap]
rs10988973	0.87[YRI][hapmap]
rs12552646	0.81[YRI][hapmap]
rs1342147	0.87[YRI][hapmap]
rs1361668	0.87[YRI][hapmap]
rs1529191	0.91[YRI][hapmap]
rs1539297	0.87[YRI][hapmap]
rs16918878	0.87[CHD][hapmap];0.87[JPT][hapmap]
rs1830454	0.96[CEU][hapmap];0.88[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1852863	0.96[CEU][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1881751	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1997367	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.94[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1997368	1.00[ASW][hapmap];0.96[CEU][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.91[LWK][hapmap];0.85[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2031035	0.90[CEU][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2057476	0.91[YRI][hapmap]
rs2181579	0.91[YRI][hapmap]
rs2416935	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2416936	0.96[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2416937	0.96[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2416938	0.83[JPT][hapmap]
rs2416940	0.88[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2416941	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2416942	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2698999	0.83[YRI][hapmap]
rs2795575	0.83[YRI][hapmap]
rs2900224	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4282626	0.96[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4452862	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4517187	0.87[YRI][hapmap]
rs4585797	0.95[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4742777	1.00[ASW][hapmap];0.96[CEU][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4742778	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4742779	0.91[YRI][hapmap]
rs4743370	0.96[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6478987	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6478990	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7022999	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7027619	0.96[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7027813	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7038506	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7039716	0.96[CEU][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs846759	0.87[YRI][hapmap]
rs846762	0.86[YRI][hapmap]
rs9299335	0.96[CEU][hapmap];0.88[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9556	STX17	cis	cerebellum	SCAN
rs9556	C9orf30	cis	cerebellum	SCAN
rs9556	STX17	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:102682600-102751400	Weak transcription	NH-A	brain
2	chr9:102686400-102750800	Weak transcription	Esophagus	oesophagus
3	chr9:102686600-102750800	Weak transcription	Gastric	stomach
4	chr9:102699800-102739800	Weak transcription	K562	blood
5	chr9:102699800-102765800	Weak transcription	Psoas Muscle	Psoas
6	chr9:102701000-102751000	Weak transcription	Fetal Intestine Small	intestine
7	chr9:102705000-102751200	Weak transcription	Brain Angular Gyrus	brain
8	chr9:102708400-102744000	Weak transcription	NHDF-Ad	bronchial
9	chr9:102711400-102765800	Weak transcription	Right Ventricle	heart
10	chr9:102711400-102769200	Weak transcription	Osteobl	bone
11	chr9:102711800-102749000	Weak transcription	Brain Germinal Matrix	brain
12	chr9:102712200-102732400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr9:102712200-102765600	Weak transcription	Brain Cingulate Gyrus	brain
14	chr9:102712400-102751000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:102713200-102765600	Weak transcription	HSMMtube	muscle
16	chr9:102714200-102749200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr9:102718000-102777600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr9:102718800-102751000	Weak transcription	Pancreas	Pancrea
19	chr9:102719000-102739400	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr9:102719000-102765400	Weak transcription	HepG2	liver
21	chr9:102720200-102733200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr9:102720200-102733600	Strong transcription	Liver	Liver
23	chr9:102720200-102736600	Strong transcription	Primary T cells from cord blood	blood
24	chr9:102720400-102746400	Weak transcription	Spleen	Spleen
25	chr9:102721600-102739600	Weak transcription	Fetal Brain Female	brain
26	chr9:102722200-102734400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr9:102722400-102751000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr9:102724000-102751600	Weak transcription	Fetal Brain Male	brain
29	chr9:102724000-102751800	Weak transcription	Fetal Kidney	kidney
30	chr9:102725200-102741800	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr9:102725400-102737400	Weak transcription	Brain Substantia Nigra	brain
32	chr9:102725400-102749000	Weak transcription	Brain Hippocampus Middle	brain
33	chr9:102725600-102732600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr9:102726200-102733200	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr9:102726400-102733400	Strong transcription	Duodenum Mucosa	Duodenum
36	chr9:102727400-102750800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:102727600-102733600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr9:102728200-102733400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr9:102728200-102738400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr9:102728400-102732800	Strong transcription	Primary B cells from cord blood	blood
41	chr9:102728800-102732600	Strong transcription	Rectal Mucosa Donor 29	rectum
42	chr9:102728800-102732800	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr9:102729200-102733400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr9:102729400-102733200	Weak transcription	HUVEC	blood vessel
45	chr9:102729400-102733600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr9:102729400-102739800	Weak transcription	A549	lung
47	chr9:102729400-102764600	Weak transcription	HSMM	muscle
48	chr9:102729600-102732400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr9:102729600-102733000	Strong transcription	Placenta	Placenta
50	chr9:102729600-102733200	Strong transcription	Adipose Nuclei	Adipose

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