Variant report

Variant	rs1130197
Chromosome Location	chr3:54666509-54666510
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:54657347..54660339-chr3:54665865..54667406,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LRTM1-3	chr3:54666151-54666883	NONHSAT090017

Variant related genes	Relation type
ENSG00000229806	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10510769	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10510770	0.87[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10510771	1.00[JPT][hapmap]
rs10510772	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11914640	1.00[ASN][1000 genomes]
rs11914780	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11914973	1.00[JPT][hapmap]
rs11920788	1.00[JPT][hapmap]
rs11924275	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11925949	1.00[JPT][hapmap]
rs12185982	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1427774	1.00[ASN][1000 genomes]
rs17054227	0.86[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17054246	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17054250	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17054291	1.00[JPT][hapmap]
rs17054293	1.00[JPT][hapmap]
rs17054340	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17815617	0.86[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17816548	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17816566	1.00[ASN][1000 genomes]
rs1863858	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2359857	0.90[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs28455661	1.00[ASN][1000 genomes]
rs2884808	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs34478567	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs41381544	1.00[ASN][1000 genomes]
rs4345041	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4358270	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs4386460	0.81[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55675480	1.00[ASN][1000 genomes]
rs55772258	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55779022	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56008232	1.00[ASN][1000 genomes]
rs56091855	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56112781	1.00[ASN][1000 genomes]
rs56209938	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56260111	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56356828	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56976748	1.00[ASN][1000 genomes]
rs57924227	1.00[ASN][1000 genomes]
rs58295654	1.00[ASN][1000 genomes]
rs59004379	1.00[ASN][1000 genomes]
rs62255527	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255532	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62255533	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255534	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255535	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255536	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62255538	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803005	0.95[CEU][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72870661	1.00[ASN][1000 genomes]
rs72870676	1.00[ASN][1000 genomes]
rs72870688	1.00[ASN][1000 genomes]
rs72872218	1.00[ASN][1000 genomes]
rs72872226	1.00[ASN][1000 genomes]
rs72872229	1.00[ASN][1000 genomes]
rs72872244	1.00[ASN][1000 genomes]
rs72872259	1.00[ASN][1000 genomes]
rs72872285	1.00[ASN][1000 genomes]
rs72874203	1.00[ASN][1000 genomes]
rs72874204	1.00[ASN][1000 genomes]
rs73068445	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737517	1.00[JPT][hapmap]
rs7624695	1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014595	chr3:53944473-54846754	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv428084	chr3:54404258-54742756	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv834700	chr3:54637374-54803896	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv525644	chr3:54653316-54709987	Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1130197	ESRG	cis	Whole Blood	GTEx

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:54654000-54667000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:54660400-54666800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:54663000-54667800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:54663200-54667400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr3:54663600-54683800	Weak transcription	Stomach Smooth Muscle	stomach
6	chr3:54663800-54667400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:54663800-54667600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:54664600-54667200	Weak transcription	HMEC	breast
9	chr3:54665200-54667000	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr3:54665200-54667200	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:54665200-54667800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:54665200-54672800	Weak transcription	Right Atrium	heart
13	chr3:54665400-54667000	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:54665400-54668200	Enhancers	Brain Germinal Matrix	brain
15	chr3:54665600-54666600	Enhancers	Fetal Brain Female	brain
16	chr3:54665800-54666800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:54665800-54667600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:54666000-54667000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:54666200-54667800	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr3:54666400-54666600	Enhancers	Brain Anterior Caudate	brain
21	chr3:54666400-54666800	Weak transcription	Fetal Brain Male	brain
22	chr3:54666400-54666800	Enhancers	NHDF-Ad	bronchial
23	chr3:54666400-54667000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:54666400-54667600	Strong transcription	H9 Cell Line	embryonic stem cell
25	chr3:54666400-54667800	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:54666400-54669000	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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