Variant report

Variant	rs2222311
Chromosome Location	chr14:72796787-72796788
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:72794559..72797059-chr14:72803417..72805844,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10146126	0.84[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10149207	0.89[YRI][hapmap]
rs11620677	0.82[ASW][hapmap];0.82[AMR][1000 genomes]
rs1356842	0.89[CEU][hapmap];0.82[YRI][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1402063	0.93[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1402064	0.93[CHB][hapmap];0.80[GIH][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1996661	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2090736	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2139596	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs2190509	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs2238195	0.94[ASW][hapmap];0.82[CEU][hapmap];0.88[GIH][hapmap];0.93[YRI][hapmap];0.87[AMR][1000 genomes]
rs2238204	0.80[AMR][1000 genomes]
rs2238206	0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2238207	0.96[TSI][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes]
rs2239244	0.81[AMR][1000 genomes]
rs2239246	0.87[CEU][hapmap];0.80[CHB][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2250557	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2250666	0.93[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2529459	0.89[CEU][hapmap]
rs2529474	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2529476	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2681724	0.86[EUR][1000 genomes]
rs2681729	0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs2681732	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2681739	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2681740	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs2681750	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs2681770	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4899430	1.00[TSI][hapmap];0.80[YRI][hapmap];0.81[AMR][1000 genomes]
rs6574061	0.80[AMR][1000 genomes]
rs6574065	0.82[AMR][1000 genomes]
rs699366	0.89[JPT][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes]
rs7151952	0.96[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes]
rs765221	0.94[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.98[LWK][hapmap];0.86[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs847331	0.81[ASW][hapmap];0.94[CEU][hapmap];0.84[LWK][hapmap];0.93[TSI][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs847334	0.89[CEU][hapmap];0.83[TSI][hapmap]
rs847346	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs847348	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs847349	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs847350	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs847360	0.80[CHD][hapmap]
rs847362	0.81[CHD][hapmap]

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	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
2	nsv948800	chr14:72462557-73150701	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2222311	TMED10	cis	parietal	SCAN
rs2222311	TTC9	cis	parietal	SCAN
rs2222311	PI16	trans	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72794400-72798200	Weak transcription	Rectal Smooth Muscle	rectum
2	chr14:72794600-72797800	Weak transcription	Colon Smooth Muscle	Colon
3	chr14:72796400-72798200	Weak transcription	Lung	lung
4	chr14:72796400-72801000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr14:72796600-72799800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr14:72796600-72801400	Enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links