Variant report

Variant	rs13112411
Chromosome Location	chr4:120992204-120992205
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:120991949-120992874	A549	lung:	n/a	chr4:120992536-120992549 chr4:120992534-120992550 chr4:120992533-120992551 chr4:120992535-120992556
2	POLR2A	chr4:120992127-120992575	MCF10A-Er-Src	breast:	n/a	n/a
3	SMC3	chr4:120992195-120992853	SK-N-SH	brain:	n/a	chr4:120992535-120992549
4	CTCF	chr4:120992100-120992250	WI-38	lung:	n/a	n/a
5	POLR2A	chr4:120991773-120992725	K562	blood:	n/a	n/a
6	RAD21	chr4:120992200-120992963	SK-N-SH	brain:	n/a	chr4:120992535-120992549 chr4:120992534-120992553 chr4:120992539-120992551

No.	Distal block	Cell Line	Cell type
1	chr4:120990955..120993835-chr4:120994776..120997866,3	K562	blood:
2	chr4:120991469..120992437-chr4:121077071..121077874,2	MCF-7	breast:
3	chr4:120990485..120993835-chr4:120994653..120998479,5	K562	blood:
4	chr4:120988391..120991014-chr4:120991976..120993821,3	MCF-7	breast:

Variant related genes	Relation type
MAD2L1	TF binding region
ENSG00000250938	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10010446	0.87[ASN][1000 genomes]
rs11727480	0.80[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11942060	0.87[ASN][1000 genomes]
rs12711084	0.80[CHB][hapmap];0.87[ASN][1000 genomes]
rs13121806	0.95[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13126018	0.80[EUR][1000 genomes]
rs13128669	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13131021	0.88[EUR][1000 genomes]
rs13136371	1.00[ASN][1000 genomes]
rs13151610	0.86[EUR][1000 genomes]
rs1362595	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs1546120	0.91[CEU][hapmap]
rs1908169	0.83[ASN][1000 genomes]
rs1972014	0.91[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28538838	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2892890	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2908988	0.91[CEU][hapmap]
rs2908989	0.91[CEU][hapmap]
rs2908990	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2934379	0.91[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3113988	0.91[CEU][hapmap];0.80[CHB][hapmap]
rs4568220	0.86[EUR][1000 genomes]
rs6534169	0.84[ASN][1000 genomes]
rs6534170	0.86[ASN][1000 genomes]
rs6810690	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6817243	0.95[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6855113	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7659231	0.81[AMR][1000 genomes];0.87[EUR][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	nsv532739	chr4:120392824-121098103	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv1007641	chr4:120884220-121555889	Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv537234	chr4:120884220-121555889	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:120989400-120992400	Enhancers	NHLF	lung
2	chr4:120989400-121012600	Weak transcription	Aorta	Aorta
3	chr4:120989600-120992400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr4:120989600-120992400	Enhancers	Osteobl	bone
5	chr4:120989600-120992800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr4:120989600-120993000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:120989800-120996400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr4:120990400-120992400	Enhancers	NHEK	skin
9	chr4:120990400-120993400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr4:120990600-120992400	Enhancers	Dnd41	blood
11	chr4:120990800-120992400	Enhancers	NHDF-Ad	bronchial
12	chr4:120990800-120992800	Enhancers	Muscle Satellite Cultured Cells	--
13	chr4:120991000-120992400	Enhancers	NH-A	brain
14	chr4:120991000-120998200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr4:120991200-120992400	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr4:120991600-120992400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr4:120991800-120994400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:120992000-120992600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr4:120992200-120992400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr4:120992200-120992400	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr4:120992200-120992400	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr4:120992200-120992400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:120992200-120992400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:120992200-120992400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
25	chr4:120992200-120992600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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