Variant report

Variant	rs17238784
Chromosome Location	chr2:210379888-210379889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 67 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10179388	1.00[GIH][hapmap];0.90[TSI][hapmap]
rs10196953	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs10197252	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs10514642	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs10514643	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs11896384	1.00[CEU][hapmap]
rs11899684	1.00[GIH][hapmap];0.90[TSI][hapmap]
rs12986617	1.00[CEU][hapmap]
rs12990915	1.00[CEU][hapmap]
rs12992468	1.00[CEU][hapmap]
rs12993084	1.00[CEU][hapmap]
rs12993506	1.00[CEU][hapmap]
rs12993627	1.00[CEU][hapmap]
rs12995238	1.00[CEU][hapmap]
rs12995429	1.00[CEU][hapmap]
rs13000954	1.00[CEU][hapmap]
rs13002255	1.00[CEU][hapmap]
rs13014332	1.00[CEU][hapmap]
rs13015584	1.00[CEU][hapmap]
rs13022394	1.00[CEU][hapmap]
rs13022724	1.00[CEU][hapmap]
rs13023473	1.00[CEU][hapmap]
rs13025539	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs13027122	1.00[CEU][hapmap]
rs13027599	1.00[CEU][hapmap]
rs13027724	0.81[TSI][hapmap]
rs13383482	0.85[EUR][1000 genomes]
rs13384979	1.00[GIH][hapmap];0.90[TSI][hapmap]
rs13394033	0.85[EUR][1000 genomes]
rs16842909	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs16842929	1.00[CEU][hapmap]
rs16842934	1.00[CEU][hapmap]
rs16843062	0.92[EUR][1000 genomes]
rs16843177	1.00[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes]
rs16843555	1.00[GIH][hapmap];0.81[TSI][hapmap]
rs17236751	1.00[CEU][hapmap]
rs17237076	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17237719	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs17237893	1.00[CEU][hapmap]
rs17238539	1.00[CEU][hapmap]
rs17239083	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17308504	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17309028	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17309518	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17316313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17316862	1.00[CEU][hapmap]
rs17316904	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs17316974	1.00[CEU][hapmap]
rs17317100	1.00[CEU][hapmap]
rs17317170	1.00[CEU][hapmap]
rs17317645	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17317756	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17745550	1.00[GIH][hapmap]
rs288063	1.00[CEU][hapmap]
rs288095	0.92[EUR][1000 genomes]
rs58195909	0.96[EUR][1000 genomes]
rs59649490	0.96[EUR][1000 genomes]
rs59999353	0.96[EUR][1000 genomes]
rs60457662	0.96[EUR][1000 genomes]
rs6756379	1.00[CEU][hapmap]
rs73067004	0.96[EUR][1000 genomes]
rs73069087	0.96[EUR][1000 genomes]
rs73069088	0.96[EUR][1000 genomes]
rs73069096	0.96[EUR][1000 genomes]
rs7577387	1.00[GIH][hapmap]
rs7603804	0.92[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834519	chr2:210271017-210400153	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs17238784	CA9	trans	lymphoblastoid	seeQTL
rs17238784	SPANXE	trans	lymphoblastoid	seeQTL
rs17238784	PRAC	trans	lymphoblastoid	seeQTL
rs17238784	MYOC	trans	lymphoblastoid	seeQTL
rs17238784	ELAVL4	trans	lymphoblastoid	seeQTL
rs17238784	KCTD14	trans	lymphoblastoid	seeQTL
rs17238784	SPANXD	trans	lymphoblastoid	seeQTL
rs17238784	HGF	trans	lymphoblastoid	seeQTL
rs17238784	LCN15	trans	lymphoblastoid	seeQTL
rs17238784	CCDC85A	trans	lymphoblastoid	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210364600-210387600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr2:210364600-210392200	Weak transcription	Pancreas	Pancrea
3	chr2:210366600-210387800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:210371400-210391000	Weak transcription	Aorta	Aorta
5	chr2:210372800-210381000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:210373000-210380000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr2:210378000-210380200	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr2:210378000-210384000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:210378800-210383200	Weak transcription	Brain Germinal Matrix	brain
10	chr2:210378800-210384000	Weak transcription	Fetal Brain Female	brain
11	chr2:210378800-210385800	Weak transcription	Fetal Brain Male	brain
12	chr2:210378800-210390200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:210379400-210382000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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