Variant report

Variant	rs2005390
Chromosome Location	chr1:119940381-119940382
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	chr1:119937462..119940451-chr17:57969185..57971965,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000108423	Chromatin interaction
ENSG00000108443	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10802090	0.92[ASN][1000 genomes]
rs10802092	0.85[EUR][1000 genomes]
rs10923802	0.92[ASN][1000 genomes]
rs10923804	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.90[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10923805	0.92[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10923808	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12035411	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038241	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12038498	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12135388	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12409531	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12740687	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12752713	0.83[JPT][hapmap]
rs1341018	0.85[EUR][1000 genomes]
rs1417604	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856887	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2224995	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2298028	0.86[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2793132	0.83[ASN][1000 genomes]
rs2854963	0.85[ASN][1000 genomes]
rs2854964	0.86[ASN][1000 genomes]
rs3765955	0.94[CHB][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs4659004	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4659169	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4659170	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4659171	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4659175	0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6428816	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6658331	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6667203	0.94[CHB][hapmap];0.85[CHD][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs6667679	0.86[ASW][hapmap];0.92[CEU][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs74112683	0.92[ASN][1000 genomes]
rs879333	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs879334	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs947127	0.92[EUR][1000 genomes]

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	nsv932014	chr1:119476480-120471049	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
2	nsv917091	chr1:119688975-120023222	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	esv34089	chr1:119752112-120072961	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1000391	chr1:119837978-120287056	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv535077	chr1:119837978-120287056	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv1004662	chr1:119847447-120154798	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
7	esv2763647	chr1:119929442-120154798	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv2599	chr1:119935023-119967748	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:119936000-119940800	Enhancers	Fetal Intestine Large	intestine
2	chr1:119937000-119945800	Weak transcription	Liver	Liver
3	chr1:119937800-119946400	Weak transcription	HepG2	liver
4	chr1:119939000-119941600	Enhancers	Fetal Intestine Small	intestine
5	chr1:119939400-119940600	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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