Variant report

Variant	rs4801313
Chromosome Location	chr19:56826958-56826959
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	STAT5A	chr19:56826417-56827107	GM12878	blood:	n/a	n/a
2	POLR2A	chr19:56825626-56827070	K562	blood:	n/a	n/a
3	MAZ	chr19:56825507-56827079	GM12878	blood:	n/a	chr19:56826866-56826875 chr19:56826870-56826879 chr19:56826045-56826054
4	CEBPB	chr19:56826717-56826977	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:56826352-56826972	HUVEC	blood vessel:	n/a	n/a
6	ZC3H11A	chr19:56826216-56827096	K562	blood:	n/a	n/a
7	PBX3	chr19:56826338-56826990	SK-N-SH	brain:	n/a	n/a
8	POLR2A	chr19:56825534-56827042	U87	brain:	n/a	n/a
9	SP1	chr19:56825609-56827000	A549	lung:	n/a	chr19:56826245-56826254 chr19:56826243-56826255 chr19:56825948-56825957 chr19:56826880-56826892 chr19:56825947-56825956 chr19:56826576-56826597 chr19:56826243-56826255 chr19:56825932-56825946 chr19:56825647-56825656 chr19:56826244-56826253 chr19:56825947-56825956
10	POLR2A	chr19:56825575-56827068	MCF-7	breast:	n/a	n/a
11	MAZ	chr19:56824862-56827211	IMR90	lung:	n/a	chr19:56826866-56826875 chr19:56826870-56826879 chr19:56826045-56826054
12	POLR2A	chr19:56825230-56826966	GM12878	blood:	n/a	n/a
13	REST	chr19:56825102-56827194	H1-neurons	neurons:	n/a	chr19:56826159-56826172 chr19:56826867-56826876
14	PAX5	chr19:56826066-56826982	GM12878	blood:	n/a	chr19:56826642-56826659
15	TBL1XR1	chr19:56826713-56827239	K562	blood:	n/a	n/a
16	GABPA	chr19:56825690-56826986	MCF-7	breast:	n/a	chr19:56825958-56825972 chr19:56825958-56825967 chr19:56825960-56825969 chr19:56825958-56825969
17	POLR2A	chr19:56825413-56827064	K562	blood:	n/a	n/a
18	MYC	chr19:56825608-56826997	K562	blood:	n/a	chr19:56826866-56826875 chr19:56826870-56826879 chr19:56826045-56826054 chr19:56826599-56826609
19	POLR2A	chr19:56825419-56826971	ProgFib	skin:	n/a	n/a
20	CREB1	chr19:56825337-56826976	HepG2	liver:	n/a	chr19:56826006-56826019
21	RUNX3	chr19:56825302-56827091	GM12878	blood:	n/a	n/a
22	JUND	chr19:56825542-56827017	Hela-S3	cervix:	n/a	chr19:56826008-56826017 chr19:56826585-56826594
23	JUN	chr19:56825246-56827380	K562	blood:	n/a	chr19:56826008-56826017 chr19:56826007-56826020 chr19:56826585-56826594
24	MAX	chr19:56825525-56827068	ECC-1	luminal epithelium:	n/a	chr19:56826866-56826875 chr19:56826870-56826879 chr19:56826045-56826054 chr19:56826599-56826609
25	CHD2	chr19:56825392-56827081	GM12878	blood:	n/a	chr19:56826752-56826762 chr19:56826747-56826757
26	POLR2A	chr19:56825447-56826990	PFSK-1	brain:	n/a	n/a
27	GABPA	chr19:56825427-56827158	A549	lung:	n/a	chr19:56825958-56825972 chr19:56825958-56825967 chr19:56825960-56825969 chr19:56825958-56825969
28	POLR2A	chr19:56825495-56826962	HUVEC	blood vessel:	n/a	n/a
29	HCFC1	chr19:56825525-56827020	K562	blood:	n/a	n/a
30	CREB1	chr19:56825473-56827033	H1-hESC	embryonic stem cell:	n/a	chr19:56826006-56826019
31	SIX5	chr19:56825630-56827027	A549	lung:	n/a	chr19:56826470-56826479 chr19:56826472-56826481
32	POLR2A	chr19:56825412-56826979	Hela-S3	cervix:	n/a	n/a
33	SIN3A	chr19:56825491-56827103	GM12878	blood:	n/a	n/a
34	NR2F2	chr19:56826312-56827174	K562	blood:	n/a	n/a
35	MAX	chr19:56825663-56827079	SK-N-SH	brain:	n/a	chr19:56826866-56826875 chr19:56826870-56826879 chr19:56826045-56826054 chr19:56826599-56826609
36	MAX	chr19:56825773-56827001	A549	lung:	n/a	chr19:56826866-56826875 chr19:56826870-56826879 chr19:56826045-56826054 chr19:56826599-56826609
37	POLR2A	chr19:56825350-56827125	HepG2	liver:	n/a	n/a
38	MTA3	chr19:56826567-56827222	GM12878	blood:	n/a	n/a
39	POLR2A	chr19:56825622-56827051	MCF-7	breast:	n/a	n/a
40	BHLHE40	chr19:56825517-56827059	K562	blood:	n/a	n/a
41	POLR2A	chr19:56825319-56827176	H1-neurons	neurons:	n/a	n/a
42	SIN3AK20	chr19:56825935-56827073	A549	lung:	n/a	n/a
43	CEBPB	chr19:56825244-56826970	IMR90	lung:	n/a	n/a
44	POLR2A	chr19:56825467-56827016	GM19193	blood:	n/a	n/a
45	POLR2A	chr19:56825520-56826971	GM12892	blood:	n/a	n/a
46	MXI1	chr19:56825196-56827042	GM12878	blood:	n/a	chr19:56826864-56826879 chr19:56826866-56826881 chr19:56826045-56826060 chr19:56826043-56826058
47	POLR2A	chr19:56825198-56827051	MCF10A-Er-Src	breast:	n/a	n/a
48	SIN3AK20	chr19:56825677-56827071	PANC-1	pancreas:	n/a	n/a
49	GTF2F1	chr19:56825333-56827149	Hela-S3	cervix:	n/a	n/a
50	GABPA	chr19:56825471-56827081	A549	lung:	n/a	chr19:56825958-56825972 chr19:56825958-56825967 chr19:56825960-56825969 chr19:56825958-56825969

No.	Distal block	Cell Line	Cell type
1	chr19:56826282..56828501-chr19:56879622..56881209,2	K562	blood:
2	chr19:56825335..56828118-chr19:56903219..56906332,4	K562	blood:
3	chr19:56825352..56829856-chr19:56831358..56835885,6	K562	blood:
4	chr19:56631390..56634909-chr19:56825062..56827444,3	MCF-7	breast:
5	chr19:56651555..56653145-chr19:56824729..56827557,2	MCF-7	breast:
6	chr19:56631391..56633030-chr19:56824712..56827583,2	K562	blood:
7	chr19:56825335..56828118-chr19:56903219..56905060,3	K562	blood:
8	chr19:56631659..56633594-chr19:56825559..56827609,3	MCF-7	breast:
9	chr19:56165049..56166864-chr19:56826052..56827910,2	K562	blood:
10	chr19:56824639..56829612-chr19:56829732..56835885,11	K562	blood:
11	chr19:56825650..56827475-chr19:56859296..56861906,3	K562	blood:
12	chr19:56612599..56616950-chr19:56825214..56827593,3	MCF-7	breast:
13	chr19:56825234..56827754-chr19:56833575..56835953,2	MCF-7	breast:
14	chr19:42363829..42364535-chr19:56826662..56827436,2	Hela-S3	cervix:
15	chr19:56152176..56154153-chr19:56826714..56828246,2	MCF-7	breast:
16	chr19:56806540..56808650-chr19:56825989..56828485,3	MCF-7	breast:
17	chr19:56654193..56655732-chr19:56826080..56828082,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF583-5	chr19:56826623-56828172	ENSG00000267549.1

Variant related genes	Relation type
ENSG00000267549	TF binding region
ZSCAN5A	TF binding region
ENSG00000267298	TF binding region
ENSG00000105372	Chromatin interaction
ENSG00000267429	Chromatin interaction
ENSG00000142409	Chromatin interaction
ENSG00000018869	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000223060	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000167685	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000131848	Chromatin interaction
ENSG00000267710	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000266907	Chromatin interaction
ENSG00000240225	Chromatin interaction
ENSG00000267454	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs6509991	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7245993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8110189	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064371	chr19:56418215-56842450	ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv1057316	chr19:56418215-56849458	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
3	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
4	nsv526325	chr19:56741186-56852035	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	nsv1058026	chr19:56799847-56833153	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
11	nsv1067261	chr19:56820571-56854916	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 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	chr19:56825000-56827000	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr19:56825000-56827000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr19:56825000-56827200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr19:56825000-56827400	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr19:56825000-56827400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr19:56825000-56827800	Active TSS	A549	lung
7	chr19:56825200-56827000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
8	chr19:56825200-56827000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:56825200-56827000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:56825200-56827000	Active TSS	Esophagus	oesophagus
11	chr19:56825200-56827000	Active TSS	Left Ventricle	heart
12	chr19:56825200-56827200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr19:56825200-56827200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr19:56825200-56827200	Active TSS	Right Ventricle	heart
15	chr19:56825200-56827400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:56825200-56827400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:56825200-56827400	Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr19:56825200-56827800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr19:56825400-56827000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr19:56825400-56827000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:56825400-56827000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr19:56825400-56827000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr19:56825400-56827000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr19:56825400-56827000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:56825400-56827000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr19:56825400-56827000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr19:56825400-56827000	Active TSS	Aorta	Aorta
28	chr19:56825400-56827000	Active TSS	Brain Substantia Nigra	brain
29	chr19:56825400-56827000	Active TSS	Fetal Intestine Small	intestine
30	chr19:56825400-56827000	Active TSS	Gastric	stomach
31	chr19:56825400-56827000	Active TSS	Right Atrium	heart
32	chr19:56825400-56827000	Active TSS	Sigmoid Colon	Sigmoid Colon
33	chr19:56825400-56827000	Active TSS	Small Intestine	intestine
34	chr19:56825400-56827000	Active TSS	GM12878-XiMat	blood
35	chr19:56825400-56827000	Active TSS	Hela-S3	cervix
36	chr19:56825400-56827000	Active TSS	HSMMtube	muscle
37	chr19:56825400-56827200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
38	chr19:56825400-56827200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:56825400-56827200	Active TSS	Ovary	ovary
40	chr19:56825400-56827400	Active TSS	Psoas Muscle	Psoas
41	chr19:56825400-56827400	Active TSS	NHDF-Ad	bronchial
42	chr19:56825400-56827600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr19:56825400-56827600	Active TSS	iPS-18 Cell Line	embryonic stem cell
44	chr19:56825400-56827600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:56825600-56827000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr19:56825600-56827000	Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr19:56825600-56827000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr19:56825600-56827000	Active TSS	Brain Angular Gyrus	brain
49	chr19:56825600-56827000	Active TSS	Brain Germinal Matrix	brain
50	chr19:56825600-56827000	Active TSS	Fetal Brain Female	brain

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