Variant report

Variant	rs12683634
Chromosome Location	chr9:98766861-98766862
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98753369..98756091-chr9:98765183..98768443,3	K562	blood:
2	chr9:98758966..98761197-chr9:98765461..98768218,3	K562	blood:
3	chr9:98758267..98760888-chr9:98765461..98767832,3	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10983321	0.84[EUR][1000 genomes]
rs10988581	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10988804	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11787559	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11790370	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11790491	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11793298	0.82[EUR][1000 genomes]
rs11794054	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12685221	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12686222	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12686457	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1360064	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16910262	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16910296	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16910298	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16910418	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1831228	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1999023	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2026032	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2069053	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34533243	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3780574	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4532708	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4742775	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4742781	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4743372	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743418	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4743436	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4743472	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7048414	0.80[ASN][1000 genomes]
rs73536517	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73656544	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7868270	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12683634	LINC00476	cis	Whole Blood	GTEx
rs12683634	LINC00476	cis	Esophagus Mucosa	GTEx
rs12683634	C9orf130	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98706400-98777400	Weak transcription	Psoas Muscle	Psoas
2	chr9:98714000-98782600	Weak transcription	HUVEC	blood vessel
3	chr9:98719200-98767800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:98719400-98767200	Weak transcription	Right Ventricle	heart
5	chr9:98719400-98771000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr9:98726400-98767800	Weak transcription	Gastric	stomach
7	chr9:98734600-98767800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr9:98734600-98782400	Weak transcription	NHEK	skin
9	chr9:98735400-98778400	Weak transcription	Hela-S3	cervix
10	chr9:98735800-98770600	Weak transcription	K562	blood
11	chr9:98735800-98771200	Weak transcription	HepG2	liver
12	chr9:98736600-98778800	Weak transcription	Fetal Brain Male	brain
13	chr9:98741800-98778600	Weak transcription	NH-A	brain
14	chr9:98744600-98768000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr9:98744800-98770800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr9:98744800-98771000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr9:98747800-98782800	Weak transcription	Fetal Kidney	kidney
18	chr9:98748000-98782600	Weak transcription	HMEC	breast
19	chr9:98748200-98771000	Weak transcription	Fetal Heart	heart
20	chr9:98748400-98767800	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr9:98748400-98767800	Weak transcription	NHLF	lung
22	chr9:98748400-98768400	Weak transcription	HSMMtube	muscle
23	chr9:98748400-98770600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr9:98748400-98782800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr9:98748600-98781200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr9:98749400-98770800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr9:98749600-98770200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:98750400-98768200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr9:98750400-98768400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr9:98750400-98771400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr9:98750400-98771400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:98750800-98771000	Weak transcription	A549	lung
33	chr9:98751600-98767800	Weak transcription	Colonic Mucosa	Colon
34	chr9:98751600-98772600	Weak transcription	Small Intestine	intestine
35	chr9:98751800-98767800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:98752400-98768600	Weak transcription	Osteobl	bone
37	chr9:98753400-98768400	Weak transcription	Left Ventricle	heart
38	chr9:98753400-98774200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr9:98753600-98768400	Weak transcription	Brain Hippocampus Middle	brain
40	chr9:98753600-98768600	Weak transcription	Esophagus	oesophagus
41	chr9:98753600-98769000	Weak transcription	Pancreas	Pancrea
42	chr9:98753600-98774400	Weak transcription	Brain Anterior Caudate	brain
43	chr9:98753800-98767800	Weak transcription	Brain Angular Gyrus	brain
44	chr9:98753800-98768400	Weak transcription	Brain Cingulate Gyrus	brain
45	chr9:98754000-98767800	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr9:98754000-98767800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr9:98754600-98770200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr9:98755800-98767800	Weak transcription	Ovary	ovary
49	chr9:98756000-98768600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr9:98757000-98767600	Weak transcription	Fetal Muscle Trunk	muscle

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