Variant report

Variant	rs4274640
Chromosome Location	chr2:48654672-48654673
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	chr2:48647192..48649423-chr2:48652404..48655156,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10208627	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10211336	0.96[ASN][1000 genomes]
rs10454133	0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10454134	0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10495951	0.87[JPT][hapmap]
rs10495952	0.87[JPT][hapmap]
rs11679523	0.87[JPT][hapmap]
rs11680719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11680916	0.86[JPT][hapmap]
rs11683639	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11683708	0.96[ASN][1000 genomes]
rs11685861	0.87[JPT][hapmap];0.82[EUR][1000 genomes]
rs11688481	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs11689622	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11690690	0.87[JPT][hapmap]
rs11690748	0.87[JPT][hapmap]
rs11690845	0.87[JPT][hapmap]
rs12105983	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13392004	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13399936	0.99[ASN][1000 genomes]
rs13400909	0.99[ASN][1000 genomes]
rs13401749	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs13401752	0.99[ASN][1000 genomes]
rs13429377	0.89[EUR][1000 genomes]
rs17037289	0.82[CHD][hapmap];0.87[JPT][hapmap]
rs17037298	0.87[JPT][hapmap]
rs17855177	0.87[JPT][hapmap]
rs4267555	0.92[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4316980	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4344965	0.87[JPT][hapmap]
rs4438532	0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4494796	0.97[ASN][1000 genomes]
rs4497915	0.89[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs4606978	0.95[CHB][hapmap];0.98[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4638844	0.92[ASN][1000 genomes]
rs55640438	0.94[ASN][1000 genomes]
rs55757090	0.93[ASN][1000 genomes]
rs55971719	0.93[ASN][1000 genomes]
rs56365822	0.86[ASN][1000 genomes]
rs58020097	0.99[ASN][1000 genomes]
rs58969359	0.99[ASN][1000 genomes]
rs58978223	0.84[ASN][1000 genomes]
rs59045263	0.82[ASN][1000 genomes]
rs60042255	0.86[ASN][1000 genomes]
rs60988618	0.95[ASN][1000 genomes]
rs61303367	0.84[ASN][1000 genomes]
rs62137018	0.85[ASN][1000 genomes]
rs62137019	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62137021	0.83[ASN][1000 genomes]
rs62137041	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6545036	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs6545039	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs66705539	0.84[ASN][1000 genomes]
rs6705802	0.87[JPT][hapmap]
rs6718068	0.87[JPT][hapmap]
rs6732196	0.92[ASN][1000 genomes]
rs6735288	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6743757	0.86[JPT][hapmap]
rs6747441	0.82[ASN][1000 genomes]
rs6749773	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72820454	0.86[ASN][1000 genomes]
rs72820474	0.97[ASN][1000 genomes]
rs72820479	0.98[ASN][1000 genomes]
rs72820484	0.99[ASN][1000 genomes]
rs72820492	0.97[ASN][1000 genomes]
rs72820494	0.99[ASN][1000 genomes]
rs72820499	0.98[ASN][1000 genomes]
rs7562069	0.87[JPT][hapmap]
rs7562816	0.87[JPT][hapmap]
rs7565792	0.81[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs7566239	0.87[JPT][hapmap]
rs7568574	0.82[ASN][1000 genomes]
rs7576964	0.82[JPT][hapmap]
rs7577237	0.87[JPT][hapmap]
rs7579932	0.86[JPT][hapmap]
rs7600794	0.87[JPT][hapmap]
rs7606104	0.87[JPT][hapmap]

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	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv524919	chr2:48649738-48658779	Enhancers Weak transcription Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4274640	PPP1R21	cis	Thyroid	GTEx
rs4274640	STON1-GTF2A1L	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48648000-48655000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:48652000-48660200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr2:48653600-48661200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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