Variant report

Variant	rs6123356
Chromosome Location	chr20:52692254-52692255
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TEAD4	chr20:52691499-52692310	A549	lung:	n/a	n/a
2	GATA3	chr20:52690431-52694002	MCF-7	breast:	n/a	chr20:52691423-52691431

No data

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

No.	Distal block	Cell Line	Cell type
1	chr20:52691602..52694513-chr20:52873450..52876265,2	MCF-7	breast:
2	chr20:52686177..52688177-chr20:52691097..52693282,3	K562	blood:
3	chr20:46414990..46416847-chr20:52691422..52694318,2	MCF-7	breast:
4	chr17:57081118..57083369-chr20:52692245..52694121,2	MCF-7	breast:
5	chr17:56768989..56770663-chr20:52691265..52693714,2	MCF-7	breast:
6	chr17:56707573..56710452-chr20:52690315..52697249,11	MCF-7	breast:
7	chr17:56735126..56737040-chr20:52692094..52694559,3	MCF-7	breast:
8	chr14:68717554..68720339-chr20:52691339..52694234,2	MCF-7	breast:
9	chr17:61042573..61045536-chr20:52690669..52693411,2	MCF-7	breast:
10	chr12:56318173..56320627-chr20:52692121..52694111,2	MCF-7	breast:

No data

Variant related genes	Relation type
BCAS1	TF binding region
ENSG00000196562	Chromatin interaction
ENSG00000064787	Chromatin interaction
ENSG00000121101	Chromatin interaction
ENSG00000263931	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000108384	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12624475	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12624494	0.94[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12624748	1.00[ASW][hapmap];0.94[CHB][hapmap];0.80[TSI][hapmap]
rs12624750	0.94[CHB][hapmap]
rs12625278	0.94[CHB][hapmap]
rs12625283	0.94[CHB][hapmap]
rs12625949	0.85[CEU][hapmap];0.84[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16998867	1.00[ASW][hapmap];0.94[CHB][hapmap];0.80[TSI][hapmap]
rs16998871	1.00[ASW][hapmap];0.94[CHB][hapmap];0.80[TSI][hapmap]
rs16998873	1.00[ASW][hapmap];0.94[CHB][hapmap];0.80[TSI][hapmap]
rs16998886	0.94[CHB][hapmap];0.81[GIH][hapmap];0.80[TSI][hapmap]
rs2020975	1.00[ASW][hapmap];0.94[CHB][hapmap]
rs2107328	0.94[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2870305	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2870306	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs290400	0.93[ASN][1000 genomes]
rs34522098	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3787544	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs3787545	0.94[CHB][hapmap]
rs3787551	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs412429	1.00[CEU][hapmap]
rs41304655	0.95[ASN][1000 genomes]
rs41308729	0.95[ASN][1000 genomes]
rs58634156	0.87[AMR][1000 genomes]
rs6123346	0.94[CHB][hapmap]
rs6123348	0.94[CHB][hapmap]
rs6123349	0.94[CHB][hapmap]
rs6123350	0.94[CHB][hapmap]
rs6123351	1.00[ASW][hapmap];0.94[CHB][hapmap];0.81[GIH][hapmap];0.80[TSI][hapmap]
rs6123352	0.94[CHB][hapmap];0.92[JPT][hapmap]
rs6123353	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6123354	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6123355	0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6127074	0.94[CHB][hapmap];0.80[TSI][hapmap]
rs6127075	1.00[ASW][hapmap];0.94[CHB][hapmap]
rs6127076	1.00[ASW][hapmap];0.94[CHB][hapmap];0.80[TSI][hapmap]
rs6127080	0.94[CHB][hapmap]
rs6127081	1.00[ASW][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap]
rs6127083	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6127084	1.00[ASW][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes]
rs6127085	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6127086	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]
rs6127088	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6127090	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130091	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130100	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73134888	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs899049	0.91[AMR][1000 genomes];0.94[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6123356	GCNT7	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52687400-52694000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr20:52690000-52693400	Enhancers	Stomach Mucosa	stomach
3	chr20:52690800-52693000	Enhancers	HepG2	liver
4	chr20:52691200-52694800	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr20:52691800-52693000	Enhancers	GM12878-XiMat	blood
6	chr20:52691800-52693400	Weak transcription	Gastric	stomach
7	chr20:52692000-52692400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr20:52692000-52693600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr20:52692200-52692800	Weak transcription	Ovary	ovary

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