Variant report

Variant	rs683829
Chromosome Location	chr9:98678164-98678165
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10121403	0.99[ASN][1000 genomes]
rs10481647	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10739632	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10739787	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10760675	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10818017	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs10983692	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10983739	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10983773	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs10983818	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12004422	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs12375861	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs12553442	1.00[ASN][1000 genomes]
rs1410783	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928253	0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2117432	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2164156	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2164157	0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2770837	0.86[ASN][1000 genomes]
rs583716	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs585223	0.95[ASN][1000 genomes]
rs591579	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs601916	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs615866	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs617884	0.93[ASN][1000 genomes]
rs631273	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs643815	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6478984	0.84[ASN][1000 genomes]
rs6479036	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs667018	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs680754	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs689627	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs689749	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs689871	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs689979	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs690222	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs690304	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs690335	1.00[ASN][1000 genomes]
rs690420	0.87[ASN][1000 genomes]
rs690563	0.92[CEU][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs700963	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7028281	0.88[ASN][1000 genomes]
rs7865593	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7868559	0.94[ASN][1000 genomes]
rs7874897	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs816671	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs816676	0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs816681	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9409321	0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs9409322	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][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	nsv482884	chr9:98530027-98691937	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv893599	chr9:98542410-98991254	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
3	nsv893600	chr9:98608989-98775459	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv1801890	chr9:98660433-98701801	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs683829	LINC00476	cis	Adipose Subcutaneous	GTEx
rs683829	CORO2A	cis	cerebellum	SCAN
rs683829	C9orf130	cis	cerebellum	SCAN
rs683829	C9orf130	cis	parietal	SCAN
rs683829	LOC57653	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98638800-98702200	Weak transcription	Pancreas	Pancrea
2	chr9:98640000-98678200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr9:98640000-98680600	Weak transcription	Colonic Mucosa	Colon
4	chr9:98640000-98685600	Weak transcription	Right Ventricle	heart
5	chr9:98640000-98718600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:98640200-98678200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr9:98642600-98680600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr9:98642800-98681800	Weak transcription	Fetal Kidney	kidney
9	chr9:98644400-98678400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr9:98644400-98685600	Weak transcription	Gastric	stomach
11	chr9:98644600-98690800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:98645600-98684200	Weak transcription	Brain Hippocampus Middle	brain
13	chr9:98645800-98678400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr9:98645800-98702200	Weak transcription	Aorta	Aorta
15	chr9:98646000-98680200	Weak transcription	K562	blood
16	chr9:98646600-98681800	Weak transcription	HSMMtube	muscle
17	chr9:98648200-98678600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr9:98649400-98694400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr9:98649400-98718600	Weak transcription	Spleen	Spleen
20	chr9:98649600-98679000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr9:98653800-98678400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr9:98655200-98679800	Weak transcription	Primary hematopoietic stem cells	blood
23	chr9:98658400-98678400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr9:98659200-98685600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr9:98659800-98684200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
26	chr9:98660000-98706000	Weak transcription	Fetal Heart	heart
27	chr9:98660200-98684000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr9:98664000-98678200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr9:98664000-98678400	Weak transcription	Fetal Intestine Small	intestine
30	chr9:98664000-98678400	Weak transcription	Fetal Stomach	stomach
31	chr9:98664000-98683200	Weak transcription	Brain Angular Gyrus	brain
32	chr9:98664000-98685600	Weak transcription	Brain Anterior Caudate	brain
33	chr9:98664000-98687400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr9:98664200-98680600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr9:98664200-98683600	Weak transcription	HMEC	breast
36	chr9:98664200-98685200	Weak transcription	Hela-S3	cervix
37	chr9:98664400-98685600	Weak transcription	NHEK	skin
38	chr9:98664800-98678400	Weak transcription	NH-A	brain
39	chr9:98669000-98681800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:98669600-98678200	Weak transcription	Fetal Brain Female	brain
41	chr9:98669800-98683600	Weak transcription	NHLF	lung
42	chr9:98670200-98678200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr9:98670400-98678200	Weak transcription	GM12878-XiMat	blood
44	chr9:98670600-98681800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr9:98670800-98678400	Weak transcription	Primary neutrophils fromperipheralblood	blood
46	chr9:98670800-98678600	Weak transcription	Lung	lung
47	chr9:98670800-98684200	Weak transcription	Fetal Brain Male	brain
48	chr9:98670800-98684600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:98670800-98687200	Weak transcription	Stomach Mucosa	stomach
50	chr9:98672000-98678200	Weak transcription	Fetal Lung	lung

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