Variant report

Variant	rs6123313
Chromosome Location	chr20:52402066-52402067
allele	G/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:26)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:26 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52401119..52404039-chr21:41758413..41760335,2	MCF-7	breast:
2	chr13:115044907..115047274-chr20:52401538..52403946,2	MCF-7	breast:
3	chr20:52401248..52403796-chr3:62303588..62306557,2	MCF-7	breast:
4	chr20:52372698..52373233-chr20:52401665..52402519,2	MCF-7	breast:
5	chr20:52401777..52404273-chr3:63855314..63857223,2	MCF-7	breast:
6	chr17:57920570..57925578-chr20:52400635..52405206,5	MCF-7	breast:
7	chr17:57920138..57922959-chr20:52400823..52403888,3	MCF-7	breast:
8	chr20:52401773..52405148-chr20:55839891..55841915,4	MCF-7	breast:
9	chr20:45986288..45987789-chr20:52401390..52404325,2	MCF-7	breast:
10	chr17:58595854..58597672-chr20:52401033..52402560,2	MCF-7	breast:
11	chr20:52394835..52397500-chr20:52399542..52403443,4	K562	blood:
12	chr20:52341497..52342164-chr20:52401978..52402911,2	MCF-7	breast:
13	chr20:52401244..52403957-chr21:44494158..44496334,2	MCF-7	breast:
14	chr20:52229221..52229858-chr20:52401611..52402610,4	MCF-7	breast:
15	chr20:52401336..52404306-chr8:103874838..103877830,2	MCF-7	breast:
16	chr20:52401623..52403995-chr20:52486040..52487259,28	MCF-7	breast:
17	chr20:52229214..52229879-chr20:52401623..52402514,2	MCF-7	breast:
18	chr2:117073210..117074730-chr20:52401599..52404302,2	MCF-7	breast:
19	chr20:52401639..52403990-chr20:52486019..52487230,15	MCF-7	breast:
20	chr20:52401075..52404235-chr20:55838784..55842042,3	MCF-7	breast:
21	chr19:1247945..1249666-chr20:52401472..52404362,3	MCF-7	breast:
22	chr20:50384014..50386808-chr20:52401448..52405357,3	MCF-7	breast:
23	chr20:52194980..52196290-chr20:52401631..52404661,16	MCF-7	breast:
24	chr20:52401294..52403111-chr7:13210219..13212096,2	MCF-7	breast:
25	chr20:52401511..52403835-chr20:55849653..55852433,2	MCF-7	breast:
26	chr20:52401888..52404343-chr20:52481570..52483956,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000155096	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000167470	Chromatin interaction
ENSG00000054793	Chromatin interaction
ENSG00000114405	Chromatin interaction
ENSG00000241472	Chromatin interaction
ENSG00000101144	Chromatin interaction
ENSG00000169062	Chromatin interaction
ENSG00000160200	Chromatin interaction
ENSG00000253320	Chromatin interaction
ENSG00000201524	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11086439	0.86[AMR][1000 genomes]
rs11086440	0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13045415	0.81[AMR][1000 genomes]
rs36080156	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4399775	0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap]
rs4811465	0.83[JPT][hapmap]
rs4811466	0.87[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs6126946	0.89[ASN][1000 genomes]
rs6126949	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6126951	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6126953	0.87[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834007	chr20:52213864-52404557	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	174 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv965888	chr20:52394959-52410541	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	33 gene(s)	inside rSNPs	diseases
8	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6123313	SNAI1	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52390200-52403400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr20:52401600-52402800	Enhancers	HepG2	liver
3	chr20:52401800-52402400	Enhancers	Rectal Mucosa Donor 29	rectum
4	chr20:52401800-52403800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr20:52401800-52403800	Enhancers	Primary B cells from peripheral blood	blood
6	chr20:52401800-52404000	Enhancers	Liver	Liver
7	chr20:52401800-52404200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:52401800-52404200	Enhancers	NHEK	skin
9	chr20:52402000-52402200	Enhancers	Esophagus	oesophagus
10	chr20:52402000-52402400	Enhancers	Pancreas	Pancrea
11	chr20:52402000-52403000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr20:52402000-52403600	Enhancers	Sigmoid Colon	Sigmoid Colon
13	chr20:52402000-52403800	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr20:52402000-52403800	Enhancers	Stomach Mucosa	stomach
15	chr20:52402000-52403800	Enhancers	GM12878-XiMat	blood
16	chr20:52402000-52404000	Flanking Active TSS	A549	lung
17	chr20:52402000-52404000	Enhancers	HMEC	breast
18	chr20:52402000-52404200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr20:52402000-52404400	Enhancers	Duodenum Mucosa	Duodenum
20	chr20:52402000-52407600	Enhancers	Placenta	Placenta

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