Variant report

Variant	rs12686222
Chromosome Location	chr9:98746609-98746610
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98745793..98747738-chr9:98750041..98751835,2	K562	blood:
2	chr9:98746100..98748264-chr9:98759830..98761515,2	MCF-7	breast:
3	chr9:98746263..98748269-chr9:98754898..98757748,2	K562	blood:
4	chr9:98636021..98638369-chr9:98744336..98747127,2	K562	blood:
5	chr9:98719153..98720916-chr9:98745927..98748838,2	K562	blood:

Variant related genes	Relation type
ENSG00000182150	Chromatin interaction
ENSG00000175611	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10988581	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10988804	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11787559	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11790370	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11790491	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11794054	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12683634	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12685221	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12686457	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1360064	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16910262	0.80[ASN][1000 genomes]
rs16910296	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs16910298	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16910418	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1831228	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1999023	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2026032	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2069053	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34533243	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3780574	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4532708	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4742775	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4742781	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743372	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4743418	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743436	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4743472	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73536517	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7868270	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12686222	LINC00476	cis	Whole Blood	GTEx
rs12686222	C9orf130	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 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	chr9:98719000-98751400	Weak transcription	Stomach Mucosa	stomach
4	chr9:98719200-98749600	Weak transcription	Fetal Intestine Small	intestine
5	chr9:98719200-98749800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr9:98719200-98752800	Weak transcription	Pancreas	Pancrea
7	chr9:98719200-98764200	Weak transcription	Spleen	Spleen
8	chr9:98719200-98767800	Weak transcription	Rectal Smooth Muscle	rectum
9	chr9:98719400-98767200	Weak transcription	Right Ventricle	heart
10	chr9:98719400-98771000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr9:98719600-98766800	Weak transcription	Colon Smooth Muscle	Colon
12	chr9:98722400-98747800	Weak transcription	Fetal Heart	heart
13	chr9:98723800-98749800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr9:98726400-98767800	Weak transcription	Gastric	stomach
15	chr9:98730600-98751200	Weak transcription	Small Intestine	intestine
16	chr9:98732200-98747400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr9:98732200-98751200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:98733000-98749600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr9:98734600-98749800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr9:98734600-98764400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr9:98734600-98767800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr9:98734600-98782400	Weak transcription	NHEK	skin
23	chr9:98735200-98751600	Weak transcription	NHDF-Ad	bronchial
24	chr9:98735400-98747200	Weak transcription	A549	lung
25	chr9:98735400-98778400	Weak transcription	Hela-S3	cervix
26	chr9:98735800-98747200	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr9:98735800-98747200	Weak transcription	HMEC	breast
28	chr9:98735800-98748400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr9:98735800-98764200	Weak transcription	Placenta	Placenta
30	chr9:98735800-98766600	Weak transcription	Stomach Smooth Muscle	stomach
31	chr9:98735800-98770600	Weak transcription	K562	blood
32	chr9:98735800-98771200	Weak transcription	HepG2	liver
33	chr9:98736000-98746800	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr9:98736000-98747200	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr9:98736000-98747400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:98736000-98747600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr9:98736000-98749800	Weak transcription	Lung	lung
38	chr9:98736000-98751400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr9:98736200-98752800	Weak transcription	Fetal Muscle Trunk	muscle
40	chr9:98736400-98747400	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr9:98736400-98747600	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr9:98736400-98749200	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr9:98736400-98751000	Weak transcription	Ovary	ovary
44	chr9:98736600-98778800	Weak transcription	Fetal Brain Male	brain
45	chr9:98736800-98747200	Weak transcription	Primary B cells from cord blood	blood
46	chr9:98737000-98766800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr9:98738800-98756400	Weak transcription	Aorta	Aorta
48	chr9:98740800-98747200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr9:98741600-98747200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr9:98741600-98747800	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links