Variant report

Variant	rs7730171
Chromosome Location	chr5:126824359-126824360
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10519929	0.85[CHD][hapmap]
rs10519930	0.85[CHD][hapmap]
rs10519938	0.81[GIH][hapmap]
rs11950427	0.81[GIH][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs17164935	0.92[CEU][hapmap]
rs17164996	0.80[GIH][hapmap]
rs17165035	0.85[CHD][hapmap]
rs17165082	0.87[CHD][hapmap]
rs17165105	0.85[CHD][hapmap]
rs17444885	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs17604615	0.92[CEU][hapmap];1.00[CHD][hapmap]
rs17604665	0.92[CEU][hapmap]
rs17604882	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs17604889	0.92[CEU][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs17604946	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs17673474	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs17673517	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs17673685	0.92[CEU][hapmap];1.00[CHD][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs17673995	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17763722	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[ASN][1000 genomes]
rs17839690	0.80[EUR][1000 genomes]
rs17839697	1.00[CHD][hapmap]
rs2408871	0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs3812053	0.92[EUR][1000 genomes]
rs3812054	1.00[CHD][hapmap]
rs3812055	0.81[GIH][hapmap]
rs41298308	0.92[EUR][1000 genomes]
rs41298312	0.92[EUR][1000 genomes]
rs57256097	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6595767	0.80[GIH][hapmap]
rs6595768	1.00[CHD][hapmap]
rs6595769	0.81[GIH][hapmap]
rs6874752	0.83[EUR][1000 genomes]
rs6882034	0.94[EUR][1000 genomes]
rs72790405	0.91[EUR][1000 genomes]
rs72790408	0.91[EUR][1000 genomes]
rs72790410	0.91[EUR][1000 genomes]
rs72790411	0.91[EUR][1000 genomes]
rs72790412	0.91[EUR][1000 genomes]
rs72790417	0.86[EUR][1000 genomes]
rs72790418	0.92[EUR][1000 genomes]
rs72790419	0.92[EUR][1000 genomes]
rs72790422	0.83[EUR][1000 genomes]
rs72790424	0.83[EUR][1000 genomes]
rs72790426	0.83[EUR][1000 genomes]
rs72790428	0.92[EUR][1000 genomes]
rs72790430	0.92[EUR][1000 genomes]
rs72790433	0.92[EUR][1000 genomes]
rs72790438	0.92[EUR][1000 genomes]
rs72790444	0.92[EUR][1000 genomes]
rs72790451	0.92[EUR][1000 genomes]
rs72790460	0.94[EUR][1000 genomes]
rs72790468	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790470	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790475	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790483	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790485	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72790487	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73786108	0.94[EUR][1000 genomes]
rs7718640	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7731380	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033607	chr5:126385181-127304459	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1019821	chr5:126658200-126934917	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv537894	chr5:126658200-126934917	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv1032587	chr5:126691103-126826978	Genic enhancers Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv830478	chr5:126721368-126937408	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7730171	SLC12A2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126789800-126830400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:126817200-126824400	Weak transcription	Aorta	Aorta
3	chr5:126822400-126827000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr5:126822600-126827000	Weak transcription	Brain Cingulate Gyrus	brain

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