Variant report

Variant	rs17237719
Chromosome Location	chr2:210366089-210366090
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	chr2:210363883..210366615-chr2:210368582..210372932,3	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10514642	1.00[CEU][hapmap];0.96[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10514643	1.00[CEU][hapmap];0.96[GIH][hapmap];0.89[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10514644	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11892351	0.91[TSI][hapmap]
rs11896384	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12986617	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12990915	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12991864	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12992067	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12992468	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12993084	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12993506	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12993627	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12995238	1.00[CEU][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12995429	1.00[CEU][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12997113	0.87[YRI][hapmap]
rs13000895	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13000954	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13002255	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13014332	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13015584	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13016157	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13022394	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13022724	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13023473	1.00[CEU][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13025539	1.00[CEU][hapmap];0.96[GIH][hapmap];0.84[LWK][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13027122	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13027280	0.87[YRI][hapmap]
rs13027599	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13027724	0.96[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13027957	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13030241	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13036178	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842909	1.00[CEU][hapmap];0.91[GIH][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842929	1.00[CEU][hapmap];0.91[GIH][hapmap];0.81[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16842934	1.00[CEU][hapmap];0.95[GIH][hapmap];0.91[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16843177	0.81[TSI][hapmap]
rs17236751	1.00[CEU][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17237893	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17238539	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs17238784	1.00[CEU][hapmap];0.81[TSI][hapmap]
rs17308504	1.00[CEU][hapmap];0.90[TSI][hapmap]
rs17316862	1.00[CEU][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17316904	1.00[CEU][hapmap];0.87[GIH][hapmap];0.88[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17316974	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17317100	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17317170	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs288063	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34128824	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34156640	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34923027	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34968429	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35273017	0.85[EUR][1000 genomes]
rs35388880	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35553764	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35781477	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35997966	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36003754	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36101555	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6756379	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71420756	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71420757	0.91[AMR][1000 genomes];1.00[EUR][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17237719	PRAC	trans	lymphoblastoid	seeQTL
rs17237719	CCDC85A	trans	lymphoblastoid	seeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:210360200-210366400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr2:210361800-210376400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:210363600-210370800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:210363600-210378400	Weak transcription	Brain Germinal Matrix	brain
5	chr2:210364600-210366200	Weak transcription	Aorta	Aorta
6	chr2:210364600-210387600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:210364600-210392200	Weak transcription	Pancreas	Pancrea
8	chr2:210365200-210366200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:210365200-210369200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:210365400-210368600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:210365800-210366200	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr2:210366000-210366400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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