Variant report

Variant	rs10423935
Chromosome Location	chr19:52800947-52800948
allele	C/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	HEY1	chr19:52800351-52801420	K562	blood:	n/a	n/a
2	POLR2A	chr19:52800020-52800972	K562	blood:	n/a	n/a
3	POLR2A	chr19:52800078-52801315	HepG2	liver:	n/a	n/a
4	MAX	chr19:52800378-52801076	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr19:52800020-52801023	GM18505	blood:	n/a	n/a
6	POLR2A	chr19:52800329-52801682	GM12878	blood:	n/a	n/a
7	MAZ	chr19:52799619-52801613	IMR90	lung:	n/a	n/a
8	POLR2A	chr19:52800325-52801117	GM12878	blood:	n/a	n/a
9	MAX	chr19:52800363-52801565	K562	blood:	n/a	n/a
10	POLR2A	chr19:52800072-52800955	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr19:52800068-52801080	GM12892	blood:	n/a	n/a
12	EGR1	chr19:52799937-52800947	K562	blood:	n/a	chr19:52800768-52800782 chr19:52800511-52800525
13	POLR2A	chr19:52799840-52801347	GM12891	blood:	n/a	n/a
14	POLR2A	chr19:52800359-52801029	K562	blood:	n/a	n/a
15	POLR2A	chr19:52799923-52801098	K562	blood:	n/a	n/a
16	ZNF263	chr19:52800466-52801072	HEK293-T-REx	kidney:	n/a	n/a
17	CEBPD	chr19:52800352-52801134	K562	blood:	n/a	n/a
18	UBTF	chr19:52800601-52801024	K562	blood:	n/a	n/a
19	BHLHE40	chr19:52800388-52801111	K562	blood:	n/a	n/a
20	POLR2A	chr19:52799967-52801511	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:52800025-52801113	HepG2	liver:	n/a	n/a
22	POLR2A	chr19:52800362-52801595	GM12878	blood:	n/a	n/a
23	REST	chr19:52799805-52801604	H1-neurons	neurons:	n/a	chr19:52800663-52800676 chr19:52800568-52800581 chr19:52800838-52800845 chr19:52801431-52801444 chr19:52800751-52800764 chr19:52801427-52801437
24	POLR2A	chr19:52800045-52801025	GM15510	blood:	n/a	n/a
25	MAX	chr19:52799746-52801246	A549	lung:	n/a	n/a
26	MTA3	chr19:52800001-52801219	GM12878	blood:	n/a	n/a
27	MAX	chr19:52800092-52801089	GM12878	blood:	n/a	n/a
28	POLR2A	chr19:52800316-52801095	HUVEC	blood vessel:	n/a	n/a
29	MAX	chr19:52800368-52801013	A549	lung:	n/a	n/a
30	POLR2A	chr19:52800358-52801016	GM12891	blood:	n/a	n/a
31	MXI1	chr19:52799569-52801627	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr19:52800021-52800962	GM18951	blood:	n/a	n/a
33	POLR2A	chr19:52800019-52801081	HL-60	blood:	n/a	n/a
34	CTCF	chr19:52800800-52800950	GM06990	blood:	n/a	n/a
35	REST	chr19:52800354-52800983	A549	lung:	n/a	chr19:52800663-52800676 chr19:52800568-52800581 chr19:52800838-52800845 chr19:52800751-52800764
36	CHD2	chr19:52800071-52801083	HepG2	liver:	n/a	n/a
37	GABPA	chr19:52800215-52801006	MCF-7	breast:	n/a	n/a
38	ELF1	chr19:52800339-52800984	GM12878	blood:	n/a	chr19:52800716-52800727
39	POLR2A	chr19:52799929-52801032	GM18526	blood:	n/a	n/a
40	HEY1	chr19:52800371-52800968	K562	blood:	n/a	n/a
41	ELF1	chr19:52799921-52800984	HCT-116	colon:	n/a	chr19:52800716-52800727
42	ELF1	chr19:52799938-52801103	GM12878	blood:	n/a	chr19:52800716-52800727
43	POLR2A	chr19:52800387-52800974	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr19:52800363-52801099	GM12892	blood:	n/a	n/a
45	POLR2A	chr19:52800286-52801329	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAX	chr19:52800365-52800957	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr19:52800335-52801112	K562	blood:	n/a	n/a
48	TAF1	chr19:52800346-52800985	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr19:52800194-52801028	HL-60	blood:	n/a	n/a
50	POLR2A	chr19:52800327-52801029	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52771242..52774496-chr19:52796154..52801198,5	MCF-7	breast:
2	chr19:52776723..52778376-chr19:52800239..52801922,2	K562	blood:
3	chr19:52799793..52802447-chr19:52803288..52807131,4	MCF-7	breast:
4	chr19:52772363..52775107-chr19:52799601..52802037,4	MCF-7	breast:
5	chr19:52799531..52802059-chr19:52803187..52805101,2	K562	blood:
6	chr19:52800699..52803892-chr19:52837325..52840976,3	MCF-7	breast:

Variant related genes	Relation type
ZNF480	TF binding region
ENSG00000198464	Chromatin interaction
ENSG00000196214	Chromatin interaction
ENSG00000167554	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10409096	1.00[EUR][1000 genomes]
rs10409142	1.00[EUR][1000 genomes]
rs10409486	0.94[EUR][1000 genomes]
rs10410297	1.00[EUR][1000 genomes]
rs10411111	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10411297	1.00[EUR][1000 genomes]
rs10416012	1.00[EUR][1000 genomes]
rs10418429	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10426029	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12462567	1.00[EUR][1000 genomes]
rs12462608	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28485851	1.00[EUR][1000 genomes]
rs28516831	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28550473	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28584863	1.00[EUR][1000 genomes]
rs28665950	1.00[EUR][1000 genomes]
rs28720915	1.00[EUR][1000 genomes]
rs34027972	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55739718	0.89[EUR][1000 genomes]
rs55798076	1.00[EUR][1000 genomes]
rs55910520	0.89[EUR][1000 genomes]
rs55995319	1.00[EUR][1000 genomes]
rs57659523	1.00[EUR][1000 genomes]
rs57659864	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59264782	1.00[EUR][1000 genomes]
rs62110413	1.00[EUR][1000 genomes]
rs62110414	1.00[EUR][1000 genomes]
rs62110443	1.00[EUR][1000 genomes]
rs62110446	1.00[EUR][1000 genomes]
rs73577187	1.00[EUR][1000 genomes]
rs73579004	1.00[EUR][1000 genomes]
rs8100167	1.00[EUR][1000 genomes]
rs8100504	1.00[EUR][1000 genomes]
rs8100650	1.00[EUR][1000 genomes]
rs8103205	1.00[EUR][1000 genomes]
rs8103336	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv833873	chr19:52788939-52937281	Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv1066537	chr19:52794424-53044977	Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv544060	chr19:52794424-53044977	ZNF genes & repeats Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
8	nsv912299	chr19:52795985-52832830	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52799600-52801000	Active TSS	Esophagus	oesophagus
2	chr19:52799600-52801000	Active TSS	Fetal Heart	heart
3	chr19:52799600-52801000	Active TSS	Gastric	stomach
4	chr19:52799600-52801000	Active TSS	Psoas Muscle	Psoas
5	chr19:52799600-52801000	Active TSS	Stomach Smooth Muscle	stomach
6	chr19:52799600-52801000	Active TSS	NH-A	brain
7	chr19:52799600-52801200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr19:52799600-52801200	Active TSS	Brain Hippocampus Middle	brain
9	chr19:52799600-52801200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:52799600-52801200	Active TSS	A549	lung
11	chr19:52799600-52801200	Active TSS	NHLF	lung
12	chr19:52799600-52801400	Active TSS	H9 Cell Line	embryonic stem cell
13	chr19:52799600-52801400	Active TSS	Fetal Intestine Small	intestine
14	chr19:52799600-52801400	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr19:52799600-52801400	Active TSS	GM12878-XiMat	blood
16	chr19:52799600-52801600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:52799600-52801600	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr19:52799600-52801600	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr19:52799600-52801600	Active TSS	Fetal Kidney	kidney
20	chr19:52799600-52801800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:52799600-52801800	Active TSS	Colonic Mucosa	Colon
22	chr19:52799800-52801000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr19:52799800-52801000	Active TSS	iPS-15b Cell Line	embryonic stem cell
24	chr19:52799800-52801000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:52799800-52801000	Active TSS	Brain Angular Gyrus	brain
26	chr19:52799800-52801000	Active TSS	Duodenum Mucosa	Duodenum
27	chr19:52799800-52801000	Active TSS	Left Ventricle	heart
28	chr19:52799800-52801000	Active TSS	Pancreas	Pancrea
29	chr19:52799800-52801000	Bivalent/Poised TSS	HepG2	liver
30	chr19:52799800-52801200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr19:52799800-52801200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr19:52799800-52801200	Active TSS	Brain Substantia Nigra	brain
33	chr19:52799800-52801200	Active TSS	Fetal Lung	lung
34	chr19:52799800-52801200	Active TSS	Right Ventricle	heart
35	chr19:52799800-52801200	Active TSS	Small Intestine	intestine
36	chr19:52799800-52801200	Active TSS	HMEC	breast
37	chr19:52799800-52801400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:52799800-52801400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr19:52799800-52801400	Active TSS	Aorta	Aorta
40	chr19:52799800-52801400	Active TSS	Ovary	ovary
41	chr19:52799800-52801600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr19:52799800-52801600	Active TSS	HUES48 Cell Line	embryonic stem cell
43	chr19:52799800-52801600	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr19:52799800-52801600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr19:52799800-52801600	Active TSS	Fetal Intestine Large	intestine
46	chr19:52799800-52801600	Active TSS	HSMM	muscle
47	chr19:52799800-52801600	Active TSS	NHDF-Ad	bronchial
48	chr19:52799800-52801800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr19:52800000-52801000	Active TSS	Primary T cells from cord blood	blood
50	chr19:52800000-52801000	Active TSS	Primary T helper naive cells from peripheral blood	blood

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