Variant report

Variant	rs62109714
Chromosome Location	chr19:36523759-36523760
allele	G/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	GATA2	chr19:36523554-36524198	SH-SY5Y	brain:	n/a	chr19:36523702-36523711
2	CTCF	chr19:36523640-36523790	GM12866	blood:	n/a	n/a
3	CTCF	chr19:36523720-36523870	AG09319	gingival:	n/a	n/a
4	YY1	chr19:36523612-36524078	SK-N-SH_RA	brain:	n/a	n/a
5	YY1	chr19:36523600-36524113	SK-N-SH_RA	brain:	n/a	chr19:36523604-36523618
6	CTCF	chr19:36523720-36523870	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr19:36523582-36524039	Gliobla	brain:	n/a	n/a
8	POLR2A	chr19:36523422-36524305	U87	brain:	n/a	n/a
9	POLR2A	chr19:36523597-36524133	ProgFib	skin:	n/a	n/a
10	YY1	chr19:36523586-36524093	H1-hESC	embryonic stem cell:	n/a	chr19:36523604-36523618
11	CTCF	chr19:36523700-36523850	AG09319	gingival:	n/a	n/a
12	CTCF	chr19:36523740-36523890	HA-sp	spinal cord:	n/a	n/a
13	ZNF263	chr19:36523671-36524206	HEK293-T-REx	kidney:	n/a	n/a
14	CTCF	chr19:36523700-36523850	HEK293	kidney:	n/a	n/a
15	POLR2A	chr19:36523305-36524172	H1-neurons	neurons:	n/a	n/a
16	CTCF	chr19:36523660-36523810	GM12873	blood:	n/a	n/a
17	CTCF	chr19:36523640-36523790	GM06990	blood:	n/a	n/a
18	POLR2A	chr19:36523696-36523822	GM12878	blood:	n/a	n/a
19	POLR2A	chr19:36523459-36524161	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr19:36523481-36524207	PFSK-1	brain:	n/a	n/a
21	CTCF	chr19:36523740-36523890	HVMF	connective:	n/a	n/a
22	CTCF	chr19:36523680-36523830	HVMF	connective:	n/a	n/a
23	SIN3A	chr19:36523322-36523952	H1-hESC	embryonic stem cell:	n/a	chr19:36523488-36523501 chr19:36523470-36523479
24	REST	chr19:36522810-36524431	H1-neurons	neurons:	n/a	chr19:36523635-36523642 chr19:36523011-36523029 chr19:36523488-36523501 chr19:36523770-36523783
25	TAF1	chr19:36523257-36524209	H1-neurons	neurons:	n/a	n/a
26	CTCF	chr19:36523740-36523890	NHLF	lung:	n/a	n/a
27	CTCF	chr19:36523700-36523850	AG10803	skin:	n/a	n/a
28	POLR2A	chr19:36523709-36524350	H1-hESC	embryonic stem cell:	n/a	n/a
29	CTCF	chr19:36523720-36523870	AoAF	blood vessel:	n/a	n/a
30	POLR2A	chr19:36523612-36524040	SK-N-SH	brain:	n/a	n/a
31	CTCF	chr19:36523720-36523870	HPF	lung:	n/a	n/a
32	CTCF	chr19:36523740-36523890	HFF-Myc	foreskin:	n/a	n/a
33	CTCF	chr19:36523700-36523850	HCPEpiC	choroid plexus:	n/a	n/a
34	POLR2A	chr19:36523277-36524115	H1-neurons	neurons:	n/a	n/a
35	CTCF	chr19:36523720-36523870	HA-sp	spinal cord:	n/a	n/a
36	POLR2A	chr19:36523644-36523815	K562	blood:	n/a	n/a
37	CTCF	chr19:36523720-36523870	AG09309	skin:	n/a	n/a
38	CTCF	chr19:36523660-36523810	GM12868	blood:	n/a	n/a
39	POLR2A	chr19:36523447-36524059	HUVEC	blood vessel:	n/a	n/a
40	NRF1	chr19:36523627-36523992	H1-hESC	embryonic stem cell:	n/a	chr19:36523789-36523800 chr19:36523786-36523800 chr19:36523789-36523798 chr19:36523791-36523800
41	CTCF	chr19:36523740-36523890	GM12864	blood:	n/a	n/a
42	POLR2A	chr19:36523642-36524188	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr19:36523669-36523890	HUVEC	blood vessel:	n/a	n/a
44	CTCF	chr19:36523740-36523890	BJ	skin:	n/a	n/a
45	CTCF	chr19:36523720-36523870	BJ	skin:	n/a	n/a
46	MAZ	chr19:36522691-36524331	IMR90	lung:	n/a	chr19:36523773-36523783 chr19:36524013-36524022
47	TAF1	chr19:36523707-36523973	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr19:36523555-36524302	U87	brain:	n/a	n/a
49	CTCF	chr19:36523700-36523850	HMF	breast:	n/a	n/a
50	CTCF	chr19:36523740-36523890	AG04449	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:36512890..36520143-chr19:36521963..36527491,9	K562	blood:

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

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs17639414	0.84[EUR][1000 genomes]
rs17706584	0.87[EUR][1000 genomes]
rs17851502	0.82[EUR][1000 genomes]
rs45567532	0.87[EUR][1000 genomes]
rs4806263	0.87[EUR][1000 genomes]
rs4806267	0.84[EUR][1000 genomes]
rs4806274	0.82[EUR][1000 genomes]
rs55884522	0.82[EUR][1000 genomes]
rs56185833	0.87[EUR][1000 genomes]
rs57658467	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57893103	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59832408	0.82[EUR][1000 genomes]
rs60078822	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61494900	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62109742	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62109747	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62109749	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62109752	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62109756	0.84[EUR][1000 genomes]
rs62109757	0.80[EUR][1000 genomes]
rs62109758	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62111360	0.82[EUR][1000 genomes]
rs62111361	0.82[EUR][1000 genomes]
rs62111377	0.82[EUR][1000 genomes]
rs6510515	0.83[AMR][1000 genomes];0.93[EUR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs62109714	WDR62	cis	Skin Sun Exposed Lower leg	GTEx
rs62109714	ENSG00000105270	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 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	chr19:36513600-36525600	Weak transcription	K562	blood
6	chr19:36515200-36527600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr19:36515400-36544600	Weak transcription	Pancreas	Pancrea
8	chr19:36516400-36532400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr19:36517000-36526400	Weak transcription	HepG2	liver
10	chr19:36518600-36524000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr19:36518800-36523800	Weak transcription	Spleen	Spleen
12	chr19:36518800-36532200	Weak transcription	A549	lung
13	chr19:36522000-36524200	Active TSS	Pancreatic Islets	Pancreatic Islet
14	chr19:36522200-36524000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr19:36522200-36524000	Active TSS	Fetal Kidney	kidney
16	chr19:36522200-36524200	Active TSS	Brain Cingulate Gyrus	brain
17	chr19:36522200-36524400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr19:36522200-36524400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr19:36522400-36524000	Enhancers	Liver	Liver
20	chr19:36522400-36524000	Active TSS	Brain Angular Gyrus	brain
21	chr19:36522400-36524000	Active TSS	NHLF	lung
22	chr19:36522600-36524000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:36522600-36524000	Active TSS	Brain Anterior Caudate	brain
24	chr19:36522800-36523800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:36522800-36523800	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr19:36522800-36524000	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr19:36522800-36524000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr19:36522800-36524000	Active TSS	Fetal Brain Female	brain
29	chr19:36522800-36524200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:36522800-36524200	Active TSS	HUES64 Cell Line	embryonic stem cell
31	chr19:36522800-36524200	Active TSS	iPS-15b Cell Line	embryonic stem cell
32	chr19:36522800-36524200	Active TSS	HSMMtube	muscle
33	chr19:36522800-36524400	Active TSS	iPS-20b Cell Line	embryonic stem cell
34	chr19:36522800-36524400	Active TSS	Rectal Smooth Muscle	rectum
35	chr19:36523000-36523800	Active TSS	H1 Cell Line	embryonic stem cell
36	chr19:36523000-36523800	Active TSS	Primary hematopoietic stem cells	blood
37	chr19:36523000-36523800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr19:36523000-36523800	Active TSS	Duodenum Mucosa	Duodenum
39	chr19:36523000-36524000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:36523000-36524000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr19:36523000-36524000	Active TSS	Muscle Satellite Cultured Cells	--
42	chr19:36523000-36524000	Active TSS	Brain Substantia Nigra	brain
43	chr19:36523000-36524000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
44	chr19:36523000-36524000	Active TSS	Ovary	ovary
45	chr19:36523000-36524000	Active TSS	NH-A	brain
46	chr19:36523000-36524000	Active TSS	Osteobl	bone
47	chr19:36523000-36524200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:36523000-36524200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:36523000-36524200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr19:36523000-36524200	Active TSS	Aorta	Aorta

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