Variant report

Variant	rs6022758
Chromosome Location	chr20:52425620-52425621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:236462991..236465947-chr20:52423163..52425916,2	MCF-7	breast:
2	chr20:52423366..52426072-chr20:55815498..55818114,2	MCF-7	breast:
3	chr17:57914402..57919000-chr20:52421915..52427149,7	MCF-7	breast:
4	chr20:52424950..52427553-chr3:89710194..89711857,2	MCF-7	breast:
5	chr20:52386923..52389172-chr20:52424998..52427663,3	K562	blood:
6	chr20:52406521..52409558-chr20:52424093..52427549,3	K562	blood:
7	chr20:52424572..52427398-chr6:58777006..58778744,2	MCF-7	breast:
8	chr20:52423838..52425788-chr8:37552737..37554558,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000199004	Chromatin interaction
ENSG00000062716	Chromatin interaction
ENSG00000183779	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs2191395	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2215401	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2215402	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2215403	0.86[CHB][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4437022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4809939	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4811470	0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs4811472	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4811473	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4811474	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6013805	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes]
rs6013806	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6013808	0.87[ASN][1000 genomes]
rs6022757	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6022759	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6022760	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6022761	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6022762	0.81[AMR][1000 genomes]
rs6022763	0.82[AMR][1000 genomes]
rs6022764	0.81[AMR][1000 genomes]
rs6022766	0.86[CHB][hapmap];0.80[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6022767	0.86[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6022768	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6022769	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6022771	0.82[AMR][1000 genomes]
rs6022772	0.82[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6022773	0.88[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6022779	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs6022782	0.82[CHB][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap]
rs6091748	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6097618	0.81[CEU][hapmap]

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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52418600-52430000	Weak transcription	Esophagus	oesophagus
2	chr20:52422000-52425800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr20:52422200-52425800	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr20:52422200-52425800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr20:52422200-52425800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr20:52422600-52431400	Weak transcription	HepG2	liver
7	chr20:52423600-52432400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr20:52423800-52425800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr20:52423800-52425800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr20:52423800-52425800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr20:52423800-52425800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr20:52423800-52425800	Weak transcription	NHEK	skin
13	chr20:52423800-52426000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr20:52423800-52430400	Weak transcription	NHDF-Ad	bronchial
15	chr20:52423800-52436200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr20:52425400-52426200	Enhancers	Brain Germinal Matrix	brain
17	chr20:52425400-52426400	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr20:52425400-52426400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr20:52425400-52426400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr20:52425600-52426200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr20:52425600-52426200	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr20:52425600-52426200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr20:52425600-52426200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr20:52425600-52426200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr20:52425600-52426200	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr20:52425600-52426400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr20:52425600-52427200	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr20:52425600-52427400	Enhancers	A549	lung

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