Variant report

Variant	rs10426002
Chromosome Location	chr19:52734546-52734547
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	POLR2A	chr19:52734418-52734591	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:52734371-52734627	H1-hESC	embryonic stem cell:	n/a	n/a
3	GATA3	chr19:52734281-52734805	SK-N-SH	brain:	n/a	chr19:52734490-52734502 chr19:52734492-52734501 chr19:52734493-52734510 chr19:52734491-52734501 chr19:52734492-52734499
4	POLR2A	chr19:52733579-52735269	GM12878	blood:	n/a	n/a
5	POLR2A	chr19:52733996-52734821	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr19:52734517-52734838	SH-SY5Y	brain:	n/a	n/a
7	FOSL2	chr19:52734269-52734885	SK-N-SH	brain:	n/a	chr19:52734454-52734462 chr19:52734454-52734462 chr19:52734455-52734462
8	POLR2A	chr19:52733968-52735570	U87	brain:	n/a	n/a
9	GATA3	chr19:52734212-52734879	SK-N-SH	brain:	n/a	chr19:52734490-52734502 chr19:52734492-52734501 chr19:52734493-52734510 chr19:52734491-52734501 chr19:52734492-52734499
10	POLR2A	chr19:52734010-52735147	GM12891	blood:	n/a	n/a
11	POLR2A	chr19:52733732-52735532	K562	blood:	n/a	n/a
12	POLR2A	chr19:52733747-52735160	SK-N-MC	brain:	n/a	n/a
13	POLR2A	chr19:52733733-52734589	GM12892	blood:	n/a	n/a
14	POLR2A	chr19:52733737-52735599	U87	brain:	n/a	n/a
15	POLR2A	chr19:52733795-52735686	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:52733857-52734746	K562	blood:	n/a	n/a
17	POLR2A	chr19:52733573-52735208	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:52733458-52735088	GM12892	blood:	n/a	n/a
19	PML	chr19:52733764-52734723	GM12878	blood:	n/a	n/a
20	NFATC1	chr19:52733709-52735153	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:52734461-52734633	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr19:52733734-52735162	GM12891	blood:	n/a	n/a
23	POLR2A	chr19:52734413-52734599	GM12878	blood:	n/a	n/a
24	POLR2A	chr19:52733730-52735455	PFSK-1	brain:	n/a	n/a
25	POLR2A	chr19:52733744-52734737	GM12892	blood:	n/a	n/a
26	MTA3	chr19:52733820-52734599	GM12878	blood:	n/a	n/a
27	POLR2A	chr19:52733571-52735207	GM12892	blood:	n/a	n/a
28	FOS	chr19:52734383-52734970	MCF10A-Er-Src	breast:	n/a	chr19:52734454-52734462 chr19:52734454-52734462 chr19:52734455-52734462
29	POLR2A	chr19:52733751-52735440	Hela-S3	cervix:	n/a	n/a
30	NFATC1	chr19:52733685-52734602	GM12878	blood:	n/a	n/a
31	POLR2A	chr19:52733765-52735139	GM12891	blood:	n/a	n/a
32	POLR2A	chr19:52733770-52734749	GM12891	blood:	n/a	n/a
33	POLR2A	chr19:52734502-52734701	HUVEC	blood vessel:	n/a	n/a
34	POLR2A	chr19:52733796-52735212	PANC-1	pancreas:	n/a	n/a
35	POLR2A	chr19:52734545-52734582	MCF-7	breast:	n/a	n/a
36	POLR2A	chr19:52733791-52735334	A549	lung:	n/a	n/a
37	POLR2A	chr19:52734373-52735098	HepG2	liver:	n/a	n/a
38	POLR2A	chr19:52734528-52734806	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52692325..52695090-chr19:52733176..52735417,3	MCF-7	breast:
2	chr19:52714640..52717140-chr19:52734016..52736347,2	K562	blood:
3	chr19:52733004..52735653-chr19:52772074..52774471,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF836-2	chr19:52734320-52734547	ENSG00000268015.1

Variant related genes	Relation type
ENSG00000268015	TF binding region
ENSG00000196214	Chromatin interaction
ENSG00000105568	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10402209	0.98[ASN][1000 genomes]
rs10402638	0.98[ASN][1000 genomes]
rs10403202	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10403283	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10403311	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10403464	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10403806	0.98[ASN][1000 genomes]
rs10404437	0.98[ASN][1000 genomes]
rs10407063	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407502	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10408119	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10411211	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412110	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10412196	0.94[ASN][1000 genomes]
rs10413012	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10413435	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10414083	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10414197	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10414423	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10414536	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10414852	0.98[ASN][1000 genomes]
rs10416785	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417033	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10417253	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10418666	0.85[ASN][1000 genomes]
rs10420207	0.87[ASN][1000 genomes]
rs10420560	0.98[ASN][1000 genomes]
rs10421440	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10421589	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10422483	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10422838	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10423125	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10425135	0.98[ASN][1000 genomes]
rs10426786	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16983598	0.98[ASN][1000 genomes]
rs16983601	0.98[ASN][1000 genomes]
rs16983603	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16983610	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17835942	0.98[EUR][1000 genomes]
rs2115074	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28444225	0.96[ASN][1000 genomes]
rs28563055	0.96[ASN][1000 genomes]
rs55751302	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55871532	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57102373	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60063830	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6509628	0.98[ASN][1000 genomes]
rs7249460	1.00[ASN][1000 genomes]
rs7255058	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7255677	0.84[ASN][1000 genomes]
rs7255737	0.98[ASN][1000 genomes]
rs7256125	0.96[ASN][1000 genomes]
rs7256216	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7256300	0.96[ASN][1000 genomes]
rs7256312	0.96[ASN][1000 genomes]
rs7256719	0.96[ASN][1000 genomes]
rs7259175	0.94[ASN][1000 genomes]
rs73935052	0.98[ASN][1000 genomes]
rs73935053	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8100048	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8100600	0.98[EUR][1000 genomes]
rs8101990	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8105432	0.98[ASN][1000 genomes]
rs8106271	0.98[EUR][1000 genomes]
rs8106544	0.91[ASN][1000 genomes]
rs8108636	0.98[ASN][1000 genomes]
rs8109061	0.82[ASN][1000 genomes]
rs8109512	0.98[ASN][1000 genomes]
rs8110857	0.98[ASN][1000 genomes]
rs8110881	0.98[ASN][1000 genomes]
rs874421	0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv962989	chr19:52732337-52742183	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52703000-52734600	Strong transcription	Fetal Stomach	stomach
2	chr19:52705000-52735200	Strong transcription	Stomach Smooth Muscle	stomach
3	chr19:52719000-52735400	ZNF genes & repeats	A549	lung
4	chr19:52723600-52735200	Strong transcription	Fetal Muscle Leg	muscle
5	chr19:52727600-52737800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:52730200-52737800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr19:52730800-52741000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr19:52731000-52736800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr19:52731000-52736800	Weak transcription	Stomach Mucosa	stomach
10	chr19:52731600-52734600	Weak transcription	Aorta	Aorta
11	chr19:52731600-52736400	Weak transcription	Fetal Heart	heart
12	chr19:52731600-52738000	Weak transcription	Fetal Brain Male	brain
13	chr19:52731600-52741000	Weak transcription	Colon Smooth Muscle	Colon
14	chr19:52731800-52735400	Weak transcription	Primary B cells from peripheral blood	blood
15	chr19:52731800-52736600	Weak transcription	HUVEC	blood vessel
16	chr19:52732000-52736000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr19:52732000-52736000	Weak transcription	Psoas Muscle	Psoas
18	chr19:52732000-52736600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr19:52732000-52740600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:52732000-52740800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:52732200-52734600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr19:52732200-52735600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr19:52732200-52736000	Weak transcription	Ovary	ovary
24	chr19:52732200-52736000	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr19:52732200-52736200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr19:52732200-52736400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:52732200-52741000	Weak transcription	Dnd41	blood
28	chr19:52732200-52741200	Weak transcription	Fetal Lung	lung
29	chr19:52732400-52734600	Weak transcription	Primary B cells from cord blood	blood
30	chr19:52732400-52735000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr19:52732400-52735200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr19:52732400-52735400	Weak transcription	Liver	Liver
33	chr19:52732400-52735400	Weak transcription	HSMMtube	muscle
34	chr19:52732400-52735400	Weak transcription	NHLF	lung
35	chr19:52732400-52735800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:52732400-52735800	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr19:52732400-52735800	Weak transcription	Left Ventricle	heart
38	chr19:52732400-52736000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr19:52732400-52736000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr19:52732400-52736400	Weak transcription	Adipose Nuclei	Adipose
41	chr19:52732400-52737800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr19:52732400-52737800	Weak transcription	HepG2	liver
43	chr19:52732400-52740200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr19:52732400-52740600	Weak transcription	Brain Angular Gyrus	brain
45	chr19:52732400-52741000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr19:52732400-52741200	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr19:52732600-52734800	Weak transcription	Esophagus	oesophagus
48	chr19:52732600-52735200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr19:52732600-52736000	Weak transcription	Spleen	Spleen
50	chr19:52732600-52736400	Weak transcription	Fetal Brain Female	brain

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