Variant report

Variant	rs17308504
Chromosome Location	chr2:210315026-210315027
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:210313244..210314912-chr2:210314992..210317272,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10179388	1.00[GIH][hapmap]
rs10514642	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs10514643	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs11892351	0.82[TSI][hapmap]
rs11896384	1.00[CEU][hapmap]
rs11899684	1.00[GIH][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];0.90[TSI][hapmap]
rs13027122	1.00[CEU][hapmap]
rs13027599	1.00[CEU][hapmap]
rs13027724	0.90[TSI][hapmap]
rs13383482	0.81[EUR][1000 genomes]
rs13384979	1.00[GIH][hapmap]
rs13394033	0.81[EUR][1000 genomes]
rs16842909	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs16842929	1.00[CEU][hapmap]
rs16842934	1.00[CEU][hapmap];0.82[TSI][hapmap]
rs16843062	0.88[EUR][1000 genomes]
rs16843177	1.00[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs17236751	1.00[CEU][hapmap]
rs17237076	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17237719	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs17237893	1.00[CEU][hapmap]
rs17238539	1.00[CEU][hapmap]
rs17238784	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17239083	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17309028	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17309518	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17316313	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17316862	1.00[CEU][hapmap]
rs17316904	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs17316974	1.00[CEU][hapmap]
rs17317100	1.00[CEU][hapmap]
rs17317170	1.00[CEU][hapmap]
rs17317645	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17317756	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs288063	1.00[CEU][hapmap]
rs288095	0.88[EUR][1000 genomes]
rs58195909	1.00[EUR][1000 genomes]
rs59649490	1.00[EUR][1000 genomes]
rs59999353	1.00[EUR][1000 genomes]
rs60457662	1.00[EUR][1000 genomes]
rs6756379	1.00[CEU][hapmap]
rs73067004	1.00[EUR][1000 genomes]
rs73069087	1.00[EUR][1000 genomes]
rs73069088	1.00[EUR][1000 genomes]
rs73069096	1.00[EUR][1000 genomes]
rs7603804	0.88[EUR][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	nsv834518	chr2:210204958-210372744	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
2	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
3	nsv1005298	chr2:210277791-210318067	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats 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
rs17308504	HGF	trans	lymphoblastoid	seeQTL
rs17308504	KCTD14	trans	lymphoblastoid	seeQTL
rs17308504	SPANXE	trans	lymphoblastoid	seeQTL
rs17308504	PRAC	trans	lymphoblastoid	seeQTL
rs17308504	ELAVL4	trans	lymphoblastoid	seeQTL
rs17308504	SPANXD	trans	lymphoblastoid	seeQTL
rs17308504	CCDC85A	trans	lymphoblastoid	seeQTL
rs17308504	LCN15	trans	lymphoblastoid	seeQTL
rs17308504	CA9	trans	lymphoblastoid	seeQTL
rs17308504	MYOC	trans	lymphoblastoid	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210306600-210337000	Weak transcription	Aorta	Aorta
2	chr2:210307400-210315400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr2:210308600-210324200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:210309000-210315800	Weak transcription	Fetal Brain Female	brain
5	chr2:210310200-210316000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr2:210312800-210322400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:210313000-210315800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:210314000-210315400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:210314400-210315400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:210314800-210317400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:210315000-210315200	Enhancers	Brain Germinal Matrix	brain

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