Variant report

Variant	rs10419962
Chromosome Location	chr19:36705797-36705798
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	MAZ	chr19:36704845-36706502	GM12878	blood:	n/a	n/a
2	TBL1XR1	chr19:36704895-36706786	K562	blood:	n/a	n/a
3	REST	chr19:36704763-36707048	H1-neurons	neurons:	n/a	chr19:36705953-36705966 chr19:36705449-36705459 chr19:36705169-36705178
4	POLR2A	chr19:36704892-36707104	PFSK-1	brain:	n/a	n/a
5	POLR2A	chr19:36705766-36706422	HepG2	liver:	n/a	n/a
6	BRCA1	chr19:36705672-36706065	HepG2	liver:	n/a	n/a
7	POLR2A	chr19:36705775-36706397	U87	brain:	n/a	n/a
8	CHD2	chr19:36704816-36706228	GM12878	blood:	n/a	chr19:36705832-36705842
9	MXI1	chr19:36704643-36707239	SK-N-SH	brain:	n/a	chr19:36706077-36706086
10	POLR2A	chr19:36705109-36706954	Hela-S3	cervix:	n/a	n/a
11	EP300	chr19:36705207-36707009	GM12878	blood:	n/a	chr19:36706180-36706193
12	RCOR1	chr19:36705132-36706347	GM12878	blood:	n/a	n/a
13	NR3C1	chr19:36705691-36706575	A549	lung:	n/a	chr19:36706029-36706050 chr19:36706174-36706187
14	POLR2A	chr19:36705009-36706569	H1-neurons	neurons:	n/a	n/a
15	YY1	chr19:36705311-36706242	HCT-116	colon:	n/a	chr19:36705833-36705844 chr19:36705488-36705499
16	CREB1	chr19:36704877-36706321	HepG2	liver:	n/a	n/a
17	MYC	chr19:36705186-36706870	K562	blood:	n/a	n/a
18	POLR2A	chr19:36704904-36707081	PFSK-1	brain:	n/a	n/a
19	NFYB	chr19:36705460-36706015	GM12878	blood:	n/a	n/a
20	CREB1	chr19:36704871-36706373	H1-hESC	embryonic stem cell:	n/a	n/a
21	MAX	chr19:36704978-36706455	A549	lung:	n/a	n/a
22	TAF1	chr19:36705237-36706477	H1-hESC	embryonic stem cell:	n/a	n/a
23	MYC	chr19:36705220-36706561	H1-hESC	embryonic stem cell:	n/a	n/a
24	TEAD4	chr19:36705697-36706355	HepG2	liver:	n/a	n/a
25	STAT3	chr19:36705257-36706024	GM12878	blood:	n/a	chr19:36705835-36705847 chr19:36705834-36705846
26	POLR2A	chr19:36705014-36706497	H1-hESC	embryonic stem cell:	n/a	n/a
27	RFX5	chr19:36705398-36706134	Hela-S3	cervix:	n/a	n/a
28	SIX5	chr19:36705434-36706096	H1-hESC	embryonic stem cell:	n/a	chr19:36705618-36705627 chr19:36705620-36705629 chr19:36705875-36705884 chr19:36705877-36705886
29	POLR2A	chr19:36705012-36708000	PANC-1	pancreas:	n/a	n/a
30	RELA	chr19:36704865-36706518	GM19099	blood:	n/a	n/a
31	POLR2A	chr19:36705281-36706486	K562	blood:	n/a	n/a
32	MXI1	chr19:36704688-36707015	IMR90	lung:	n/a	chr19:36706077-36706086
33	POLR2A	chr19:36705747-36707001	GM12891	blood:	n/a	n/a
34	TBP	chr19:36705209-36706618	GM12878	blood:	n/a	n/a
35	MAX	chr19:36704752-36706489	ECC-1	luminal epithelium:	n/a	n/a
36	EP300	chr19:36705224-36706968	K562	blood:	n/a	chr19:36706180-36706193
37	E2F6	chr19:36705082-36706374	K562	blood:	n/a	chr19:36706084-36706091 chr19:36706084-36706091 chr19:36705449-36705460 chr19:36706012-36706021 chr19:36706084-36706091
38	SIN3AK20	chr19:36705267-36706244	H1-hESC	embryonic stem cell:	n/a	n/a
39	KAP1	chr19:36704865-36706406	HEK293	kidney:	n/a	n/a
40	PML	chr19:36705136-36706541	K562	blood:	n/a	n/a
41	MYC	chr19:36705782-36706347	MCF-7	breast:	n/a	n/a
42	NFIC	chr19:36705130-36706350	HepG2	liver:	n/a	n/a
43	SP1	chr19:36704766-36707089	A549	lung:	n/a	chr19:36705832-36705844 chr19:36705496-36705509 chr19:36705494-36705506 chr19:36706940-36706950 chr19:36705496-36705505 chr19:36706940-36706949 chr19:36705495-36705504 chr19:36706940-36706950 chr19:36706939-36706951 chr19:36706941-36706950 chr19:36705829-36705843 chr19:36705833-36705842 chr19:36706940-36706949 chr19:36705494-36705506 chr19:36706939-36706951
44	YY1	chr19:36705290-36706436	H1-hESC	embryonic stem cell:	n/a	chr19:36705833-36705844 chr19:36705488-36705499
45	YY1	chr19:36705325-36706544	SK-N-SH_RA	brain:	n/a	chr19:36705833-36705844 chr19:36705488-36705499
46	CTCF	chr19:36705760-36705910	SK-N-SH_RA	brain:	n/a	n/a
47	NFIC	chr19:36705377-36706057	ECC-1	luminal epithelium:	n/a	n/a
48	GTF2F1	chr19:36705484-36706483	H1-hESC	embryonic stem cell:	n/a	n/a
49	MAFK	chr19:36705022-36706459	K562	blood:	n/a	n/a
50	POLR2A	chr19:36704947-36707096	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:36705772-36705822	MCF-7	breast:	n/a
2	chr19:36705772-36705822	AG09309	skin:	n/a
3	chr19:36705772-36705822	HUVEC	blood vessel:	n/a
4	chr19:36705772-36705822	NT2-D1	testis:	n/a
5	chr19:36705772-36705822	A549	lung:	n/a
6	chr19:36705772-36705822	SK-N-MC	brain:	n/a
7	chr19:36705772-36705822	HCT-116	colon:	n/a
8	chr19:36705772-36705822	H1-hESC	embryonic stem cell:	embryo
9	chr19:36705772-36705822	HRCEpiC	kidney:	n/a
10	chr19:36705772-36705822	AG10803	skin:	n/a
11	chr19:36705772-36705822	GM12878	blood:	n/a
12	chr19:36705772-36705822	AG09319	gingival:	n/a
13	chr19:36705772-36705822	NHBE	bronchial:	n/a
14	chr19:36705772-36705822	Caco-2	colon:	n/a
15	chr19:36705772-36705822	NB4	blood:	n/a
16	chr19:36705772-36705822	HMEC	breast:	n/a
17	chr19:36705772-36705822	LNCaP	prostate:	n/a
18	chr19:36705772-36705822	CMK	blood:	n/a
19	chr19:36705772-36705822	SK-N-SH	brain:	n/a
20	chr19:36705772-36705822	HNPCEpiC	eye:	n/a
21	chr19:36705772-36705822	HRPEpiC	eye:	n/a
22	chr19:36705772-36705822	HPAEpiC	pulmonary alveolar:	n/a
23	chr19:36705772-36705822	GM19239	blood:	n/a
24	chr19:36705772-36705822	HRE	kidney:	n/a
25	chr19:36705772-36705822	MCF10A-Er-Src	breast:	n/a
26	chr19:36705772-36705822	HepG2	liver:	n/a
27	chr19:36705772-36705822	BJ	skin:	n/a
28	chr19:36705772-36705822	NHDF-neo	bronchial:	n/a
29	chr19:36705772-36705822	ovcar-3	ovarian:	n/a
30	chr19:36705772-36705822	PANC-1	pancreas:	n/a
31	chr19:36705772-36705822	SAEC	small airway:	n/a
32	chr19:36705772-36705822	HL-60	blood:	n/a
33	chr19:36705772-36705822	T-47D	breast:	n/a
34	chr19:36705772-36705822	SK-N-SH_RA	brain:	n/a
35	chr19:36705772-36705822	Jurkat	blood:	n/a
36	chr19:36705772-36705822	ProgFib	skin:	n/a
37	chr19:36705772-36705822	GM12891	blood:	n/a
38	chr19:36705772-36705822	BE2_C	brain:	n/a
39	chr19:36705772-36705822	Hepatocyte	liver:	n/a
40	chr19:36705772-36705822	IMR90	lung:	fetal
41	chr19:36705772-36705822	HAEpiC	amniotic membrane:	n/a
42	chr19:36705772-36705822	Hela-S3	cervix:	n/a
43	chr19:36705772-36705822	NH-A	brain:	n/a
44	chr19:36705772-36705822	SKMC	muscle:	n/a
45	chr19:36705772-36705822	RPTEC	kidney:	n/a
46	chr19:36705772-36705822	HEK293	kidney:	embryo
47	chr19:36705772-36705822	HEEpiC	esophagus:	n/a
48	chr19:36705772-36705822	AoSMC	blood vessel:	n/a
49	chr19:36705772-36705822	GM12892	blood:	n/a
50	chr19:36705772-36705822	HIPEpiC	eye:	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:36679317..36682281-chr19:36704526..36707611,3	MCF-7	breast:
2	chr19:36705785..36707917-chr19:36719166..36721745,2	K562	blood:
3	chr19:36630278..36632151-chr19:36704046..36706551,3	MCF-7	breast:
4	chr19:36704317..36708058-chr19:36719298..36721271,3	MCF-7	breast:
5	chr19:36630466..36632159-chr19:36704253..36707369,3	K562	blood:
6	chr19:36630738..36632299-chr19:36705733..36707758,2	MCF-7	breast:
7	chr19:36704032..36706423-chr19:36978429..36980490,2	MCF-7	breast:
8	chr19:36705734..36706510-chr9:130566042..130566934,2	Hela-S3	cervix:
9	chr19:36704170..36706461-chr19:36978975..36980989,3	K562	blood:
10	chr19:36704361..36705921-chr19:37063810..37066277,2	K562	blood:
11	chr19:36629887..36633258-chr19:36704150..36708473,10	K562	blood:
12	chr19:36705027..36707515-chr19:37176765..37178367,2	MCF-7	breast:
13	chr19:36635772..36637555-chr19:36705789..36707718,2	K562	blood:

Variant related genes	Relation type
ZNF146	TF binding region
ZNF565	TF binding region
ZNF565	CpG island
ZNF146	CpG island
ENSG00000267309	Chromatin interaction
ENSG00000136877	Chromatin interaction
ENSG00000186020	Chromatin interaction
ENSG00000225975	Chromatin interaction
ENSG00000233527	Chromatin interaction
ENSG00000264276	Chromatin interaction
ENSG00000186017	Chromatin interaction
ENSG00000167635	Chromatin interaction
ENSG00000126247	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10405434	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10414444	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10414754	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10415692	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10418472	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10419778	1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10425424	1.00[AMR][1000 genomes]
rs11878240	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11882807	1.00[ASW][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap];1.00[AMR][1000 genomes]
rs12104412	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13345802	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56214452	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57994318	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61326559	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73612167	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36704000-36707400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr19:36704600-36707200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:36704600-36707200	Active TSS	NH-A	brain
4	chr19:36704600-36707400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr19:36704600-36707400	Active TSS	A549	lung
6	chr19:36704600-36707600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:36704600-36707800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr19:36704600-36708000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:36704800-36706600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr19:36704800-36706800	Active TSS	Aorta	Aorta
11	chr19:36704800-36707000	Active TSS	Pancreatic Islets	Pancreatic Islet
12	chr19:36704800-36707400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr19:36704800-36707600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr19:36704800-36707600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr19:36704800-36707600	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr19:36704800-36707600	Active TSS	Psoas Muscle	Psoas
17	chr19:36704800-36707800	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr19:36704800-36707800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr19:36704800-36708400	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr19:36705000-36706800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr19:36705000-36706800	Active TSS	Small Intestine	intestine
22	chr19:36705000-36707000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr19:36705000-36707000	Active TSS	Muscle Satellite Cultured Cells	--
24	chr19:36705000-36707000	Active TSS	Fetal Intestine Large	intestine
25	chr19:36705000-36707000	Active TSS	Fetal Intestine Small	intestine
26	chr19:36705000-36707000	Active TSS	Ovary	ovary
27	chr19:36705000-36707000	Active TSS	NHDF-Ad	bronchial
28	chr19:36705000-36707400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr19:36705000-36707600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr19:36705000-36707800	Active TSS	HSMMtube	muscle
31	chr19:36705200-36706200	Active TSS	Fetal Heart	heart
32	chr19:36705200-36706400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
33	chr19:36705200-36706600	Active TSS	Primary monocytes fromperipheralblood	blood
34	chr19:36705200-36706600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:36705200-36706600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:36705200-36706600	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr19:36705200-36706600	Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr19:36705200-36706600	Active TSS	Brain Angular Gyrus	brain
39	chr19:36705200-36706600	Active TSS	Brain Anterior Caudate	brain
40	chr19:36705200-36706600	Active TSS	Brain Substantia Nigra	brain
41	chr19:36705200-36706600	Active TSS	Colon Smooth Muscle	Colon
42	chr19:36705200-36706600	Active TSS	Thymus	Thymus
43	chr19:36705200-36706800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:36705200-36706800	Active TSS	Brain Hippocampus Middle	brain
45	chr19:36705200-36706800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:36705200-36706800	Active TSS	Esophagus	oesophagus
47	chr19:36705200-36706800	Active TSS	Gastric	stomach
48	chr19:36705200-36706800	Active TSS	Lung	lung
49	chr19:36705200-36706800	Active TSS	Pancreas	Pancrea
50	chr19:36705200-36706800	Active TSS	Sigmoid Colon	Sigmoid Colon

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