Variant report

Variant	rs6127086
Chromosome Location	chr20:52687795-52687796
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr20:52683721-52688026	A549	lung:	n/a	chr20:52684379-52684388
2	NR2F2	chr20:52683737-52688780	MCF-7	breast:	n/a	n/a
3	NR2F2	chr20:52682851-52688769	MCF-7	breast:	n/a	n/a
4	MAX	chr20:52682798-52688785	MCF-7	breast:	n/a	chr20:52685611-52685621

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:56706894..56712075-chr20:52682647..52687928,11	MCF-7	breast:
2	chr17:56734849..56737585-chr20:52685762..52689219,5	MCF-7	breast:
3	chr20:52205396..52212193-chr20:52682424..52689159,12	MCF-7	breast:
4	chr20:46130482..46132590-chr20:52685698..52688265,2	MCF-7	breast:
5	chr17:56734557..56739323-chr20:52682038..52691817,18	MCF-7	breast:
6	chr20:52554098..52560340-chr20:52684210..52688448,9	MCF-7	breast:
7	chr20:45946563..45948166-chr20:52686092..52688175,2	MCF-7	breast:
8	chr20:52610588..52612438-chr20:52687506..52690025,2	MCF-7	breast:
9	chr20:52682759..52688435-chr20:55837866..55842743,7	MCF-7	breast:
10	chr1:149222502..149226607-chr20:52685912..52688117,3	MCF-7	breast:
11	chr20:52643673..52645639-chr20:52687051..52688962,2	MCF-7	breast:
12	chr17:56769193..56771346-chr20:52687697..52690270,2	MCF-7	breast:
13	chr17:56706875..56710932-chr20:52683217..52688645,17	MCF-7	breast:

No data

Variant related genes	Relation type
MIR4756	TF binding region
BCAS1	TF binding region
ENSG00000267882	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000101040	Chromatin interaction
ENSG00000124151	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000266826	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000171940	Chromatin interaction
ENSG00000108384	Chromatin interaction
ENSG00000121101	Chromatin interaction
ENSG00000064787	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs12624475	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12624494	0.89[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12624748	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs12624750	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs12625278	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs12625283	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs12625949	0.87[CEU][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16998867	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs16998871	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs16998873	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs16998886	0.89[CHB][hapmap]
rs2020975	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs2107328	0.89[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2870305	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2870306	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs290400	0.91[ASN][1000 genomes]
rs34522098	0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3787544	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs3787545	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs3787551	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs412429	1.00[CEU][hapmap]
rs41304655	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41308729	0.96[ASN][1000 genomes]
rs58634156	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6123346	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs6123348	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs6123349	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs6123350	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs6123351	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs6123352	0.89[CHB][hapmap];0.92[JPT][hapmap]
rs6123353	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6123354	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6123355	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6123356	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6127074	0.89[CHB][hapmap]
rs6127075	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs6127076	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs6127080	0.89[CHB][hapmap];1.00[YRI][hapmap]
rs6127081	0.94[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs6127083	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6127084	1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6127085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6127088	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6127089	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6127090	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73130091	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73130100	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73134888	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs899049	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
3	nsv912944	chr20:52681759-52693614	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region miRNA	31 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52687200-52691600	Weak transcription	Gastric	stomach
2	chr20:52687400-52687800	Enhancers	A549	lung
3	chr20:52687400-52688000	Enhancers	HepG2	liver
4	chr20:52687400-52690000	Weak transcription	Fetal Intestine Large	intestine
5	chr20:52687400-52690400	Weak transcription	Fetal Intestine Small	intestine
6	chr20:52687400-52694000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr20:52687600-52687800	Enhancers	Rectal Mucosa Donor 29	rectum
8	chr20:52687600-52688400	Enhancers	Rectal Mucosa Donor 31	rectum
9	chr20:52687600-52688600	Enhancers	Stomach Mucosa	stomach
10	chr20:52687600-52691200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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