Variant report

Variant	rs12502190
Chromosome Location	chr4:78308601-78308602
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	chr4:78307066..78309627-chr4:78338398..78341247,3	MCF-7	breast:
2	chr4:78307688..78309988-chr4:78313564..78315382,2	K562	blood:

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10000203	0.82[CEU][hapmap];0.93[CHB][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10021013	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10022216	0.95[ASN][1000 genomes]
rs10023142	0.82[CEU][hapmap]
rs10024634	0.95[ASN][1000 genomes]
rs10025816	0.82[CEU][hapmap];0.93[CHB][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10031333	0.93[YRI][hapmap]
rs10031995	0.82[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.97[ASN][1000 genomes]
rs10034168	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11724731	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs1559121	0.82[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap]
rs17002568	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs17002573	0.93[ASN][1000 genomes]
rs17002574	0.82[CEU][hapmap]
rs17002575	0.93[ASN][1000 genomes]
rs17002578	0.82[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs17002614	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17002672	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs1962027	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28408985	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28470829	0.98[ASN][1000 genomes]
rs28509428	0.98[ASN][1000 genomes]
rs28510834	0.98[ASN][1000 genomes]
rs28558753	0.98[ASN][1000 genomes]
rs28640182	0.97[ASN][1000 genomes]
rs28659994	0.92[EUR][1000 genomes]
rs2866283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2866286	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28715173	0.85[EUR][1000 genomes]
rs28771770	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28821633	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28822468	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28844066	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28886989	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3886412	0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4146559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4426805	0.82[CEU][hapmap];0.93[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4447887	0.98[ASN][1000 genomes]
rs4586976	0.92[EUR][1000 genomes]
rs4643843	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4859826	1.00[CEU][hapmap];0.94[CHB][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs56704522	0.93[ASN][1000 genomes]
rs57255185	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57851138	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57854205	0.93[ASN][1000 genomes]
rs58210020	0.98[ASN][1000 genomes]
rs58493318	0.98[ASN][1000 genomes]
rs58763343	0.96[ASN][1000 genomes]
rs59017002	0.98[ASN][1000 genomes]
rs59225688	0.98[ASN][1000 genomes]
rs59548585	0.98[ASN][1000 genomes]
rs59817506	0.98[ASN][1000 genomes]
rs60084947	0.98[ASN][1000 genomes]
rs60847680	0.98[ASN][1000 genomes]
rs60994753	0.97[ASN][1000 genomes]
rs61041046	0.98[ASN][1000 genomes]
rs61482056	0.98[ASN][1000 genomes]
rs61559911	0.98[ASN][1000 genomes]
rs6819777	0.82[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs6832224	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6843981	0.82[CEU][hapmap];0.88[CHB][hapmap]
rs6849731	0.82[CEU][hapmap];0.81[CHB][hapmap]
rs6850445	0.80[EUR][1000 genomes]
rs72859841	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72859843	0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72859844	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7657699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap]
rs7666881	0.93[ASN][1000 genomes]
rs9307270	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9994349	1.00[CEU][hapmap];0.94[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006017	chr4:78139780-78312974	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1010450	chr4:78182037-78317840	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1004824	chr4:78188691-78312974	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	esv1845782	chr4:78237955-78321598	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv829974	chr4:78240718-78415642	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	esv3442840	chr4:78277532-78309591	Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv594698	chr4:78291876-78334483	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	nsv967998	chr4:78301212-78311035	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12502190	SLC16A1	trans	cerebellum	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:78307000-78308800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr4:78307000-78308800	Weak transcription	Fetal Muscle Leg	muscle
3	chr4:78307200-78308800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr4:78308200-78311200	Weak transcription	Fetal Intestine Large	intestine

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