Variant report

Variant	rs34533243
Chromosome Location	chr9:98601997-98601998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:98601662..98603295-chr9:98609133..98611273,2	K562	blood:
2	chr9:98591010..98593309-chr9:98600980..98602755,2	MCF-7	breast:
3	chr9:98599925..98602235-chr9:98637374..98639294,2	MCF-7	breast:
4	chr9:98600432..98602813-chr9:98612011..98614211,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182150	Chromatin interaction
ENSG00000175611	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10983321	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10988581	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10988804	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11787559	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11790370	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11790491	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11793298	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11794054	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12683634	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12685221	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12686222	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12686457	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1360064	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16910262	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16910296	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16910298	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16910418	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1831228	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1999023	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2026032	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2069053	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3780574	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4532708	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4742775	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742781	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4743372	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4743417	0.91[AFR][1000 genomes]
rs4743418	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4743436	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4743472	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7048414	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73536517	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73656544	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7868270	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893598	chr9:98508628-98645674	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs34533243	LINC00476	cis	Esophagus Mucosa	GTEx
rs34533243	LINC00476	cis	Whole Blood	GTEx
rs34533243	C9orf130	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:98594000-98611000	Weak transcription	Colonic Mucosa	Colon
2	chr9:98594400-98610000	Weak transcription	Fetal Stomach	stomach
3	chr9:98594600-98610000	Weak transcription	Fetal Intestine Small	intestine
4	chr9:98596200-98616400	Weak transcription	Fetal Brain Female	brain
5	chr9:98596200-98619200	Weak transcription	Fetal Heart	heart
6	chr9:98596400-98602200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr9:98596400-98619400	Weak transcription	Right Ventricle	heart
8	chr9:98598400-98604000	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:98599200-98614400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr9:98601600-98602000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr9:98601600-98602000	Enhancers	Lung	lung
12	chr9:98601600-98602000	Enhancers	Stomach Mucosa	stomach
13	chr9:98601600-98602800	Enhancers	Ovary	ovary
14	chr9:98601800-98602000	Enhancers	Aorta	Aorta
15	chr9:98601800-98602000	Enhancers	Fetal Muscle Leg	muscle
16	chr9:98601800-98602000	Enhancers	Left Ventricle	heart
17	chr9:98601800-98602200	Weak transcription	Right Atrium	heart
18	chr9:98601800-98602400	Weak transcription	Small Intestine	intestine
19	chr9:98601800-98602600	Enhancers	Psoas Muscle	Psoas
20	chr9:98601800-98602800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:98601800-98603200	Enhancers	Fetal Lung	lung

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