Variant report

Variant	rs57893103
Chromosome Location	chr19:36526709-36526710
allele	A/G
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	EP300	chr19:36526370-36526928	K562	blood:	n/a	n/a
2	USF1	chr19:36526578-36526869	K562	blood:	n/a	n/a
3	GATA3	chr19:36526432-36526856	MCF-7	breast:	n/a	chr19:36526556-36526567 chr19:36526784-36526795
4	NR2F2	chr19:36526419-36526936	K562	blood:	n/a	n/a
5	RCOR1	chr19:36526368-36527299	K562	blood:	n/a	n/a
6	MAX	chr19:36526535-36526851	K562	blood:	n/a	chr19:36526734-36526743
7	TEAD4	chr19:36526489-36526999	K562	blood:	n/a	n/a
8	CEBPD	chr19:36526504-36526933	K562	blood:	n/a	n/a
9	ELF1	chr19:36526441-36526782	K562	blood:	n/a	n/a
10	GATA1	chr19:36526256-36527250	K562	blood:	n/a	chr19:36526556-36526567 chr19:36526784-36526795 chr19:36526964-36526971
11	JUND	chr19:36526432-36526848	K562	blood:	n/a	n/a
12	GATA2	chr19:36526395-36526829	K562	blood:	n/a	chr19:36526556-36526567 chr19:36526784-36526795
13	MYC	chr19:36526470-36526909	K562	blood:	n/a	chr19:36526734-36526743
14	IRF1	chr19:36526555-36526750	K562	blood:	n/a	chr19:36526703-36526712
15	PML	chr19:36526593-36526986	K562	blood:	n/a	n/a
16	GATA2	chr19:36526377-36526818	K562	blood:	n/a	chr19:36526556-36526567 chr19:36526784-36526795
17	MAZ	chr19:36526411-36526875	K562	blood:	n/a	chr19:36526734-36526743
18	POLR2A	chr19:36526571-36526849	K562	blood:	n/a	n/a
19	TEAD4	chr19:36526316-36527068	K562	blood:	n/a	n/a
20	TAL1	chr19:36526444-36527012	K562	blood:	n/a	n/a
21	POLR2A	chr19:36526419-36526954	K562	blood:	n/a	n/a
22	HDAC2	chr19:36526404-36526919	K562	blood:	n/a	chr19:36526676-36526690
23	GATA2	chr19:36526442-36526783	SH-SY5Y	brain:	n/a	chr19:36526556-36526567
24	EGR1	chr19:36526473-36526942	K562	blood:	n/a	n/a
25	GATA2	chr19:36526398-36526946	K562	blood:	n/a	chr19:36526556-36526567 chr19:36526784-36526795
26	MAX	chr19:36526434-36526896	K562	blood:	n/a	chr19:36526734-36526743
27	EGR1	chr19:36526584-36526834	K562	blood:	n/a	n/a
28	MYC	chr19:36526445-36526948	K562	blood:	n/a	chr19:36526734-36526743
29	RCOR1	chr19:36526377-36527005	K562	blood:	n/a	n/a
30	TBL1XR1	chr19:36526474-36526945	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36506976..36509848-chr19:36525241..36526846,2	K562	blood:
2	chr19:36508348..36511238-chr19:36524542..36526846,2	K562	blood:
3	chr19:36510063..36511736-chr19:36525610..36527833,2	MCF-7	breast:
4	chr19:36512890..36520143-chr19:36521963..36527491,9	K562	blood:
5	chr19:36524837..36527233-chr19:36544073..36546693,3	K562	blood:
6	chr19:36526205..36528558-chr19:36530375..36532258,2	K562	blood:
7	chr19:36518073..36521044-chr19:36525057..36527255,2	K562	blood:

Variant related genes	Relation type
CLIP3	TF binding region
ENSG00000075702	Chromatin interaction
ENSG00000105270	Chromatin interaction
ENSG00000161277	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs17639414	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17706584	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17851502	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs45567532	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4806263	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4806267	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4806274	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55884522	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs56185833	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs57658467	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58995551	0.91[AMR][1000 genomes]
rs59832408	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60078822	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61494900	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61496921	0.91[AMR][1000 genomes]
rs62109714	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62109742	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62109747	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62109749	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62109752	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62109756	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62109757	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62109758	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62111360	0.85[EUR][1000 genomes]
rs62111361	0.85[EUR][1000 genomes]
rs62111377	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6510515	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8103791	0.91[AMR][1000 genomes]
rs8113579	0.91[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	nsv911641	chr19:36473677-36536938	Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs57893103	WDR62	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36506400-36544400	Weak transcription	GM12878-XiMat	blood
2	chr19:36506800-36532400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:36507000-36532200	Weak transcription	Hela-S3	cervix
4	chr19:36508800-36532400	Weak transcription	NHEK	skin
5	chr19:36515200-36527600	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr19:36515400-36544600	Weak transcription	Pancreas	Pancrea
7	chr19:36516400-36532400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr19:36518800-36532200	Weak transcription	A549	lung
9	chr19:36524000-36529400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr19:36524000-36532000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr19:36524000-36532000	Weak transcription	Psoas Muscle	Psoas
12	chr19:36524000-36537000	Weak transcription	Small Intestine	intestine
13	chr19:36524200-36527400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr19:36524200-36528400	Weak transcription	Right Ventricle	heart
15	chr19:36524200-36528600	Weak transcription	Adipose Nuclei	Adipose
16	chr19:36524200-36529800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr19:36524200-36530000	Weak transcription	Fetal Intestine Large	intestine
18	chr19:36524200-36530000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr19:36524200-36530200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr19:36524200-36530200	Weak transcription	Ovary	ovary
21	chr19:36524200-36530400	Weak transcription	Colonic Mucosa	Colon
22	chr19:36524200-36531600	Weak transcription	Placenta	Placenta
23	chr19:36524200-36532000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr19:36524200-36532200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr19:36524200-36532200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr19:36524200-36532200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr19:36524200-36532200	Weak transcription	NHLF	lung
28	chr19:36524200-36532400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr19:36524200-36532400	Weak transcription	HSMMtube	muscle
30	chr19:36524200-36533200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:36524200-36543800	Weak transcription	Left Ventricle	heart
32	chr19:36524200-36544000	Weak transcription	Primary B cells from cord blood	blood
33	chr19:36524200-36544400	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr19:36524200-36544400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr19:36524200-36544400	Weak transcription	Aorta	Aorta
36	chr19:36524400-36527000	Strong transcription	Fetal Intestine Small	intestine
37	chr19:36524400-36529000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr19:36524400-36529000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr19:36524400-36529800	Weak transcription	Brain Hippocampus Middle	brain
40	chr19:36524400-36532200	Weak transcription	Fetal Kidney	kidney
41	chr19:36524400-36532200	Weak transcription	NHDF-Ad	bronchial
42	chr19:36524400-36532400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:36524400-36532400	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr19:36524400-36532400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:36524400-36532400	Weak transcription	Colon Smooth Muscle	Colon
46	chr19:36524400-36532400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr19:36524400-36533000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr19:36524400-36534800	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr19:36524400-36535000	Weak transcription	Brain Angular Gyrus	brain
50	chr19:36524400-36537200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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