Variant report

Variant	rs62109752
Chromosome Location	chr19:36560620-36560621
allele	C/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	FOXA2	chr19:36560397-36560817	A549	lung:	n/a	n/a
2	PAX5	chr19:36560493-36560924	GM12878	blood:	n/a	n/a
3	PAX5	chr19:36560428-36560929	GM12878	blood:	n/a	n/a
4	SETDB1	chr19:36560432-36560629	U2OS	brain:	n/a	n/a
5	PAX5	chr19:36560585-36560872	GM12878	blood:	n/a	n/a
6	PAX5	chr19:36560503-36560900	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:36560538-36560834	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36559947..36561874-chr19:36564837..36567073,2	K562	blood:
2	chr19:36560163..36561818-chr19:36605064..36607311,2	MCF-7	breast:

Variant related genes	Relation type
WDR62	TF binding region
ENSG00000105258	Chromatin interaction
ENSG00000105254	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs17639414	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17706584	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17851502	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs45567532	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4806263	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4806267	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4806274	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55884522	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs56185833	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs57658467	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs57893103	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58995551	0.88[AMR][1000 genomes]
rs59832408	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60078822	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61494900	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61496921	0.88[AMR][1000 genomes]
rs62109714	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62109742	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62109747	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62109749	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62109756	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62109757	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62109758	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62111360	0.87[EUR][1000 genomes]
rs62111361	0.87[EUR][1000 genomes]
rs62111377	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6510515	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8103791	0.88[AMR][1000 genomes]
rs8113579	0.88[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36546400-36577600	Weak transcription	Esophagus	oesophagus
2	chr19:36546400-36584000	Weak transcription	Right Atrium	heart
3	chr19:36546600-36572400	Weak transcription	Lung	lung
4	chr19:36546600-36602200	Weak transcription	Colonic Mucosa	Colon
5	chr19:36546600-36604800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr19:36546800-36572000	Weak transcription	Primary T cells from cord blood	blood
7	chr19:36546800-36572800	Weak transcription	Primary B cells from cord blood	blood
8	chr19:36546800-36572800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr19:36546800-36580200	Weak transcription	Fetal Kidney	kidney
10	chr19:36546800-36588000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr19:36546800-36592200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr19:36546800-36601400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr19:36547000-36561200	Weak transcription	NH-A	brain
14	chr19:36547400-36561200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr19:36547400-36562000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr19:36547600-36584200	Weak transcription	Fetal Heart	heart
17	chr19:36548200-36596400	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr19:36548400-36571000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:36548600-36560800	Weak transcription	HUVEC	blood vessel
20	chr19:36548800-36567800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr19:36549600-36566600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr19:36549600-36567200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:36552000-36561600	Weak transcription	Brain Angular Gyrus	brain
24	chr19:36552000-36572400	Weak transcription	Liver	Liver
25	chr19:36555000-36593000	Weak transcription	Fetal Lung	lung
26	chr19:36556000-36601600	Weak transcription	Pancreas	Pancrea
27	chr19:36556600-36562200	Weak transcription	HSMM	muscle
28	chr19:36557200-36561200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr19:36558000-36562400	Weak transcription	Left Ventricle	heart
30	chr19:36558000-36562400	Weak transcription	Right Ventricle	heart
31	chr19:36558200-36561200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr19:36558200-36572400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr19:36558800-36561200	Weak transcription	Osteobl	bone
34	chr19:36558800-36574000	Weak transcription	Gastric	stomach
35	chr19:36559000-36562200	Weak transcription	HepG2	liver
36	chr19:36559000-36562800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr19:36559000-36572400	Weak transcription	Placenta	Placenta
38	chr19:36559200-36560800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr19:36559200-36560800	Weak transcription	Hela-S3	cervix
40	chr19:36559200-36561000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr19:36559200-36561200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:36559200-36561200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr19:36559200-36561200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:36559200-36561200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
45	chr19:36559200-36561200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr19:36559200-36561200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr19:36559200-36561200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr19:36559200-36561200	Weak transcription	Thymus	Thymus
49	chr19:36559200-36561200	Weak transcription	A549	lung
50	chr19:36559200-36561200	Weak transcription	HMEC	breast

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