Variant report

Variant	rs2288856
Chromosome Location	chr19:56879974-56879975
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:110)
CpG islands
(count:61)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr19:56879230-56880062	K562	blood:	n/a	chr19:56879874-56879885 chr19:56879872-56879887 chr19:56879431-56879440 chr19:56879873-56879886
2	TAF1	chr19:56879352-56880082	K562	blood:	n/a	n/a
3	CTCF	chr19:56879920-56880070	GM12871	blood:	n/a	n/a
4	MAX	chr19:56879243-56880204	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr19:56879206-56880394	H1-hESC	embryonic stem cell:	n/a	n/a
6	CTCF	chr19:56879920-56880070	GM12864	blood:	n/a	n/a
7	POLR2A	chr19:56879400-56879996	GM12892	blood:	n/a	n/a
8	MAX	chr19:56879250-56879985	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr19:56879421-56879980	K562	blood:	n/a	n/a
10	POLR2A	chr19:56879131-56880092	H1-neurons	neurons:	n/a	n/a
11	TAF1	chr19:56879224-56880118	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr19:56879960-56880110	HBMEC	blood vessel:	n/a	n/a
13	TAF1	chr19:56879353-56880042	ECC-1	luminal epithelium:	n/a	n/a
14	NRF1	chr19:56878841-56880268	SK-N-SH	brain:	n/a	chr19:56879429-56879440 chr19:56879430-56879444 chr19:56879430-56879441 chr19:56879427-56879441 chr19:56879430-56879439
15	TBP	chr19:56879307-56880000	K562	blood:	n/a	n/a
16	CTCF	chr19:56879900-56880050	NHEK	skin:	n/a	n/a
17	MAX	chr19:56879278-56880040	H1-hESC	embryonic stem cell:	n/a	n/a
18	POLR2A	chr19:56879356-56879996	HL-60	blood:	n/a	n/a
19	FOXA2	chr19:56879830-56880089	HepG2	liver:	n/a	n/a
20	POLR2A	chr19:56879217-56880032	K562	blood:	n/a	n/a
21	MAFK	chr19:56879461-56880017	K562	blood:	n/a	n/a
22	POLR2A	chr19:56879377-56880033	HUVEC	blood vessel:	n/a	n/a
23	ZMIZ1	chr19:56879464-56880075	K562	blood:	n/a	n/a
24	POLR2A	chr19:56879363-56880006	GM12878	blood:	n/a	n/a
25	CREB1	chr19:56879241-56880148	HepG2	liver:	n/a	n/a
26	CHD2	chr19:56879523-56880080	HepG2	liver:	n/a	n/a
27	CTCF	chr19:56879960-56880110	HVMF	connective:	n/a	n/a
28	TAF7	chr19:56879326-56880040	H1-hESC	embryonic stem cell:	n/a	n/a
29	BHLHE40	chr19:56879287-56880148	K562	blood:	n/a	n/a
30	FOXA1	chr19:56879830-56880169	T-47D	breast:	n/a	n/a
31	CTCF	chr19:56879900-56880050	HMF	breast:	n/a	n/a
32	CTCF	chr19:56879960-56880110	HRPEpiC	eye:	n/a	n/a
33	JUND	chr19:56879337-56880170	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr19:56879198-56880000	K562	blood:	n/a	n/a
35	TCF12	chr19:56879308-56880063	A549	lung:	n/a	n/a
36	MYC	chr19:56879219-56880002	K562	blood:	n/a	n/a
37	CTCF	chr19:56879940-56880090	HMF	breast:	n/a	n/a
38	MAX	chr19:56879279-56879976	HepG2	liver:	n/a	n/a
39	POLR2A	chr19:56879356-56880075	HUVEC	blood vessel:	n/a	n/a
40	E2F6	chr19:56879184-56880102	A549	lung:	n/a	chr19:56879431-56879440
41	BHLHE40	chr19:56879383-56880162	HepG2	liver:	n/a	n/a
42	CTCF	chr19:56879920-56880070	AoAF	blood vessel:	n/a	n/a
43	FOXA1	chr19:56879871-56880155	T-47D	breast:	n/a	n/a
44	MAX	chr19:56879303-56880030	K562	blood:	n/a	n/a
45	POLR2A	chr19:56879180-56880207	H1-hESC	embryonic stem cell:	n/a	n/a
46	CHD1	chr19:56879753-56880228	H1-hESC	embryonic stem cell:	n/a	n/a
47	MAZ	chr19:56879318-56880003	K562	blood:	n/a	n/a
48	POLR2A	chr19:56879378-56879989	ECC-1	luminal epithelium:	n/a	n/a
49	POLR2A	chr19:56879297-56879996	H1-hESC	embryonic stem cell:	n/a	n/a
50	BRCA1	chr19:56879484-56880015	H1-hESC	embryonic stem cell:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr19:56879933-56879983	AoSMC	blood vessel:	n/a
2	chr19:56879933-56879983	AG09319	gingival:	n/a
3	chr19:56879933-56879983	SK-N-MC	brain:	n/a
4	chr19:56879933-56879983	PANC-1	pancreas:	n/a
5	chr19:56879933-56879983	HCF	heart:	n/a
6	chr19:56879933-56879983	PrEC	prostate:	n/a
7	chr19:56879933-56879983	HL-60	blood:	n/a
8	chr19:56879933-56879983	AG10803	skin:	n/a
9	chr19:56879933-56879983	NHDF-neo	bronchial:	n/a
10	chr19:56879933-56879983	RPTEC	kidney:	n/a
11	chr19:56879933-56879983	NHBE	bronchial:	n/a
12	chr19:56879933-56879983	IMR90	lung:	fetal
13	chr19:56879933-56879983	HRE	kidney:	n/a
14	chr19:56879933-56879983	HCPEpiC	choroid plexus:	n/a
15	chr19:56879933-56879983	HUVEC	blood vessel:	n/a
16	chr19:56879933-56879983	CMK	blood:	n/a
17	chr19:56879933-56879983	GM12892	blood:	n/a
18	chr19:56879933-56879983	MCF10A-Er-Src	breast:	n/a
19	chr19:56879933-56879983	BJ	skin:	n/a
20	chr19:56879933-56879983	HEK293	kidney:	embryo
21	chr19:56879933-56879983	K562	blood:	n/a
22	chr19:56879933-56879983	GM12878	blood:	n/a
23	chr19:56879933-56879983	T-47D	breast:	n/a
24	chr19:56879933-56879983	BE2_C	brain:	n/a
25	chr19:56879933-56879983	GM06990	blood:	n/a
26	chr19:56879933-56879983	NB4	blood:	n/a
27	chr19:56879933-56879983	ECC-1	luminal epithelium:	n/a
28	chr19:56879933-56879983	PFSK-1	brain:	n/a
29	chr19:56879933-56879983	Caco-2	colon:	n/a
30	chr19:56879933-56879983	Hela-S3	cervix:	n/a
31	chr19:56879933-56879983	HAEpiC	amniotic membrane:	n/a
32	chr19:56879933-56879983	U87	brain:	n/a
33	chr19:56879933-56879983	ovcar-3	ovarian:	n/a
34	chr19:56879933-56879983	AG09309	skin:	n/a
35	chr19:56879933-56879983	HRCEpiC	kidney:	n/a
36	chr19:56879933-56879983	AG04449	skin:	fetal
37	chr19:56879933-56879983	SK-N-SH	brain:	n/a
38	chr19:56879933-56879983	HMEC	breast:	n/a
39	chr19:56879933-56879983	ProgFib	skin:	n/a
40	chr19:56879933-56879983	LNCaP	prostate:	n/a
41	chr19:56879933-56879983	HNPCEpiC	eye:	n/a
42	chr19:56879933-56879983	HEEpiC	esophagus:	n/a
43	chr19:56879933-56879983	Hepatocyte	liver:	n/a
44	chr19:56879933-56879983	SK-N-SH_RA	brain:	n/a
45	chr19:56879933-56879983	HRPEpiC	eye:	n/a
46	chr19:56879933-56879983	NT2-D1	testis:	n/a
47	chr19:56879933-56879983	Jurkat	blood:	n/a
48	chr19:56879933-56879983	HCM	heart:	n/a
49	chr19:56879933-56879983	GM19239	blood:	n/a
50	chr19:56879933-56879983	HepG2	liver:	n/a

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56832521..56834727-chr19:56879587..56882084,2	K562	blood:
2	chr19:56878151..56881655-chr19:56903333..56906269,7	K562	blood:
3	chr19:56878056..56881655-chr19:56903333..56906269,5	K562	blood:
4	chr19:56826282..56828501-chr19:56879622..56881209,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000267606	TF binding region
ZSCAN5A	TF binding region
ZNF542	TF binding region
ENSG00000267606	CpG island
ZNF542	CpG island
ZSCAN5A	CpG island
ENSG00000267549	Chromatin interaction
ENSG00000131848	Chromatin interaction
ENSG00000018869	Chromatin interaction
ENSG00000266907	Chromatin interaction
ENSG00000267454	Chromatin interaction
ENSG00000200646	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1017102	0.89[CHB][hapmap];0.92[CHD][hapmap]
rs10401898	0.89[ASN][1000 genomes]
rs10405914	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10413341	0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10418348	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10419074	0.83[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10419213	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12608563	0.80[ASN][1000 genomes]
rs12610246	0.89[CHB][hapmap];0.92[CHD][hapmap];0.80[ASN][1000 genomes]
rs12981331	0.89[CHB][hapmap];0.92[CHD][hapmap];0.83[ASN][1000 genomes]
rs12983342	0.88[CHB][hapmap]
rs12983411	0.89[ASN][1000 genomes]
rs2304123	0.89[CHB][hapmap];0.92[CHD][hapmap];0.86[ASN][1000 genomes]
rs2304125	0.89[CHB][hapmap];0.92[CHD][hapmap];0.86[ASN][1000 genomes]
rs2304126	0.89[CHB][hapmap];0.80[ASN][1000 genomes]
rs2304127	0.89[CHB][hapmap];0.92[CHD][hapmap]
rs4334405	0.95[ASN][1000 genomes]
rs4801717	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8111942	0.89[CHB][hapmap];0.92[CHD][hapmap]

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	nsv912516	chr19:56601298-56981382	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	93 gene(s)	inside rSNPs	diseases
2	nsv949121	chr19:56754719-57591038	ZNF genes & repeats Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
3	nsv1062341	chr19:56794070-57273332	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
4	nsv544094	chr19:56794070-57273332	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
5	nsv1056713	chr19:56799151-57265682	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
6	nsv544095	chr19:56799151-57265682	Strong transcription ZNF genes & repeats Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56878800-56880200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:56878800-56880200	Active TSS	Brain Cingulate Gyrus	brain
3	chr19:56878800-56880400	Active TSS	iPS-18 Cell Line	embryonic stem cell
4	chr19:56878800-56880600	Active TSS	H1 Cell Line	embryonic stem cell
5	chr19:56878800-56880600	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:56878800-56880600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr19:56878800-56880800	Active TSS	ES-I3 Cell Line	embryonic stem cell
8	chr19:56879000-56880000	Active TSS	Primary T cells from cord blood	blood
9	chr19:56879000-56880000	Active TSS	Primary T helper cells fromperipheralblood	blood
10	chr19:56879000-56880000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
11	chr19:56879000-56880000	Active TSS	Adipose Nuclei	Adipose
12	chr19:56879000-56880000	Active TSS	Brain Angular Gyrus	brain
13	chr19:56879000-56880000	Active TSS	Stomach Smooth Muscle	stomach
14	chr19:56879000-56880000	Active TSS	NH-A	brain
15	chr19:56879000-56880200	Active TSS	Primary T helper naive cells from peripheral blood	blood
16	chr19:56879000-56880200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr19:56879000-56880200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr19:56879000-56880200	Active TSS	Brain Germinal Matrix	brain
19	chr19:56879000-56880200	Active TSS	Brain Inferior Temporal Lobe	brain
20	chr19:56879000-56880200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr19:56879000-56880200	Active TSS	Brain Substantia Nigra	brain
22	chr19:56879000-56880200	Active TSS	Colon Smooth Muscle	Colon
23	chr19:56879000-56880200	Active TSS	Duodenum Smooth Muscle	Duodenum
24	chr19:56879000-56880200	Active TSS	Fetal Brain Male	brain
25	chr19:56879000-56880200	Active TSS	Fetal Brain Female	brain
26	chr19:56879000-56880200	Active TSS	Fetal Lung	lung
27	chr19:56879000-56880200	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr19:56879000-56880200	Active TSS	Rectal Smooth Muscle	rectum
29	chr19:56879000-56880200	Active TSS	Right Atrium	heart
30	chr19:56879000-56880200	Active TSS	HSMM	muscle
31	chr19:56879000-56880200	Active TSS	Osteobl	bone
32	chr19:56879000-56880400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr19:56879000-56880400	Active TSS	iPS-15b Cell Line	embryonic stem cell
34	chr19:56879000-56880400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:56879000-56880400	Active TSS	Muscle Satellite Cultured Cells	--
36	chr19:56879000-56880400	Active TSS	Fetal Kidney	kidney
37	chr19:56879000-56880400	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr19:56879000-56880400	Active TSS	NHEK	skin
39	chr19:56879000-56880600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr19:56879000-56880600	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr19:56879000-56880600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr19:56879000-56880600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr19:56879000-56880600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr19:56879000-56880600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr19:56879000-56880800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr19:56879000-56880800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:56879000-56880800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr19:56879000-56880800	Active TSS	HepG2	liver
49	chr19:56879000-56880800	Active TSS	HSMMtube	muscle
50	chr19:56879000-56880800	Active TSS	NHDF-Ad	bronchial

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