Variant report

Variant	rs4666398
Chromosome Location	chr2:20658519-20658520
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20640108..20658716-chr2:20812153..20855311,258	MCF-7	breast:
2	chr2:20652225..20654236-chr2:20656975..20659900,2	K562	blood:
3	chr2:20656537..20659242-chr2:20696316..20698465,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118960	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1002162	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10856799	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11898154	0.83[EUR][1000 genomes]
rs11901246	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13021908	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1453051	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs168195	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1872070	0.82[EUR][1000 genomes]
rs2348707	0.83[EUR][1000 genomes]
rs342106	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342107	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs342110	0.93[EUR][1000 genomes]
rs342111	0.90[EUR][1000 genomes]
rs342114	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs342116	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4666397	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4666401	0.83[EUR][1000 genomes]
rs6531240	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6704834	0.83[EUR][1000 genomes]
rs7601359	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv455830	chr2:20621404-20659862	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv581166	chr2:20621404-20659862	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
3	nsv873717	chr2:20625174-20756900	Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv873718	chr2:20627875-20752152	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
5	nsv873719	chr2:20628882-20756900	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
6	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	nsv873720	chr2:20645835-20756900	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
8	nsv873721	chr2:20645835-20759789	Enhancers Bivalent Enhancer Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
9	nsv873722	chr2:20652507-20705910	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20650800-20659000	Weak transcription	Pancreas	Pancrea
2	chr2:20653200-20666200	Weak transcription	Brain Anterior Caudate	brain
3	chr2:20653400-20666400	Weak transcription	Brain Substantia Nigra	brain
4	chr2:20653400-20674000	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr2:20654000-20665400	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:20656000-20658800	Enhancers	HepG2	liver
7	chr2:20656200-20671800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr2:20657200-20658600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:20657200-20665800	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:20657600-20658600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr2:20657600-20659200	Enhancers	Stomach Mucosa	stomach
12	chr2:20658000-20659200	Enhancers	Gastric	stomach
13	chr2:20658200-20659000	Enhancers	Esophagus	oesophagus
14	chr2:20658400-20665400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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