Variant report

Variant	rs2215403
Chromosome Location	chr20:52427476-52427477
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:63951602..63953984-chr20:52426825..52428778,2	MCF-7	breast:
2	chr20:52424950..52427553-chr3:89710194..89711857,2	MCF-7	breast:
3	chr20:52386923..52389172-chr20:52424998..52427663,3	K562	blood:
4	chr20:52406521..52409558-chr20:52424093..52427549,3	K562	blood:
5	chr16:85492452..85494325-chr20:52425691..52428180,2	MCF-7	breast:
6	chr20:52426559..52428423-chr4:43882290..43883810,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168439	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11086441	0.80[AMR][1000 genomes]
rs2097849	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2191395	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215401	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215402	0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2904374	0.80[EUR][1000 genomes]
rs4416274	0.81[CHB][hapmap]
rs4437022	0.86[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs4491782	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4618108	0.85[CHB][hapmap]
rs4809939	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4811470	0.86[CHB][hapmap];0.80[AMR][1000 genomes]
rs4811471	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs4811472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4811473	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4811474	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6013803	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6013805	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6013806	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6013808	0.80[AMR][1000 genomes]
rs6013809	0.84[CEU][hapmap];0.82[TSI][hapmap]
rs6022757	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6022758	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6022759	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6022760	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6022761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6022762	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6022763	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6022764	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6022766	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6022767	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6022768	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6022769	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6022770	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6022771	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6022772	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6022773	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6022779	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6022782	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6064007	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6064008	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6068679	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6068680	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6068681	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6091748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6123316	0.81[CHB][hapmap]
rs6126963	0.81[CHB][hapmap]
rs6126964	0.81[CHB][hapmap]
rs6126970	0.81[CHB][hapmap]
rs6126971	0.81[CHB][hapmap]
rs6126972	0.81[CHB][hapmap]
rs6126973	0.80[CHB][hapmap]
rs6126975	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1057509	chr20:52390002-52431309	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	nsv1063442	chr20:52400519-52428220	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
6	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 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	chr20:52418600-52430000	Weak transcription	Esophagus	oesophagus
2	chr20:52422600-52431400	Weak transcription	HepG2	liver
3	chr20:52423600-52432400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr20:52423800-52430400	Weak transcription	NHDF-Ad	bronchial
5	chr20:52423800-52436200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr20:52426200-52430400	Weak transcription	NHEK	skin
7	chr20:52426200-52456200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr20:52426400-52431400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:52426400-52436000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr20:52427200-52434600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr20:52427400-52427600	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr20:52427400-52427600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr20:52427400-52427800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr20:52427400-52430000	Weak transcription	A549	lung

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