Variant report

Variant	rs6126963
Chromosome Location	chr20:52413734-52413735
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:56708001..56710383-chr20:52413455..52415056,2	MCF-7	breast:
2	chr20:52411903..52414095-chr20:52416977..52419626,3	K562	blood:
3	chr20:52411996..52414093-chr20:55824314..55826589,2	MCF-7	breast:
4	chr20:52406598..52408941-chr20:52412585..52415507,2	K562	blood:
5	chr17:58469385..58471176-chr20:52411862..52414045,2	MCF-7	breast:
6	chr11:62572508..62574533-chr20:52412014..52414129,2	MCF-7	breast:
7	chr1:145382749..145383537-chr20:52413556..52414517,2	MCF-7	breast:
8	chr17:57914792..57918180-chr20:52413541..52418064,4	MCF-7	breast:
9	chr17:56707901..56710252-chr20:52413457..52417061,3	MCF-7	breast:
10	chr11:122931494..122933593-chr20:52412455..52415144,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000062716	Chromatin interaction
ENSG00000170832	Chromatin interaction
ENSG00000162231	Chromatin interaction
ENSG00000225563	Chromatin interaction
ENSG00000201558	Chromatin interaction
ENSG00000109971	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000141371	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1117558	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1117559	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12625415	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2215403	0.81[CHB][hapmap]
rs3764716	0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4330164	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4361184	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4416274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4416275	0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4618108	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4619669	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4811470	0.86[CHB][hapmap]
rs4811472	0.81[CHB][hapmap]
rs56808127	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58281268	0.92[ASN][1000 genomes]
rs6022761	0.81[CHB][hapmap]
rs6022766	0.81[CHB][hapmap]
rs6022767	0.81[CHB][hapmap]
rs6022772	0.81[CHB][hapmap]
rs6022773	0.82[CHB][hapmap]
rs6022779	0.81[CHB][hapmap]
rs6091748	0.85[CHB][hapmap]
rs6123316	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6126956	0.84[CEU][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6126958	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6126962	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6126964	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6126969	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6126970	0.93[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6126971	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6126972	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6126973	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs62208437	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67468076	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][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	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	nsv586221	chr20:52392390-52418987	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
6	nsv1064299	chr20:52395560-52420612	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
7	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
8	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6126963	BCAS4	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52404200-52414400	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr20:52404200-52415600	Weak transcription	Fetal Intestine Large	intestine
3	chr20:52406600-52417200	Weak transcription	K562	blood
4	chr20:52410600-52416400	Weak transcription	Liver	Liver
5	chr20:52411000-52415600	Weak transcription	Pancreas	Pancrea
6	chr20:52411600-52415600	Weak transcription	Esophagus	oesophagus
7	chr20:52411600-52415600	Weak transcription	NHEK	skin
8	chr20:52411800-52415600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:52411800-52421400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr20:52412000-52415400	Weak transcription	HMEC	breast
11	chr20:52412000-52417400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr20:52412200-52421600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr20:52412600-52415400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr20:52413600-52413800	Enhancers	Colonic Mucosa	Colon
15	chr20:52413600-52414000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr20:52413600-52414000	Enhancers	A549	lung
17	chr20:52413600-52416400	Enhancers	HepG2	liver

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