Variant report

Variant	rs12973009
Chromosome Location	chr19:56825895-56825896
allele	C/T
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	YY1	chr19:56825695-56826619	GM12878	blood:	n/a	chr19:56826158-56826169
2	THAP1	chr19:56825873-56826319	K562	blood:	n/a	n/a
3	POLR2A	chr19:56825626-56827070	K562	blood:	n/a	n/a
4	MAZ	chr19:56825507-56827079	GM12878	blood:	n/a	chr19:56826866-56826875 chr19:56826870-56826879 chr19:56826045-56826054
5	JUND	chr19:56825825-56826516	HepG2	liver:	n/a	chr19:56826008-56826017
6	POLR2A	chr19:56825415-56826379	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr19:56825698-56826320	HepG2	liver:	n/a	n/a
8	MYC	chr19:56825586-56826819	MCF10A-Er-Src	breast:	n/a	chr19:56826045-56826054 chr19:56826599-56826609
9	ELF1	chr19:56825830-56826732	A549	lung:	n/a	chr19:56826232-56826243 chr19:56825993-56826005 chr19:56826231-56826244
10	CEBPD	chr19:56825745-56826380	HepG2	liver:	n/a	n/a
11	ARID3A	chr19:56825542-56826504	HepG2	liver:	n/a	n/a
12	BACH1	chr19:56825552-56826050	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr19:56825670-56825992	GM12891	blood:	n/a	n/a
14	POLR2A	chr19:56825766-56826350	A549	lung:	n/a	n/a
15	EBF1	chr19:56824518-56826341	GM12878	blood:	n/a	chr19:56825320-56825331
16	POLR2A	chr19:56825419-56826307	K562	blood:	n/a	n/a
17	ETS1	chr19:56825835-56826946	K562	blood:	n/a	chr19:56826537-56826553 chr19:56826286-56826299 chr19:56826230-56826240 chr19:56825967-56825980 chr19:56826232-56826241 chr19:56826232-56826241 chr19:56826541-56826550 chr19:56826541-56826550
18	JUN	chr19:56825847-56826191	HepG2	liver:	n/a	chr19:56826008-56826017 chr19:56826007-56826020
19	PML	chr19:56825666-56825980	GM12878	blood:	n/a	n/a
20	POLR2A	chr19:56825534-56827042	U87	brain:	n/a	n/a
21	CUX1	chr19:56825700-56826218	GM12878	blood:	n/a	n/a
22	SIN3AK20	chr19:56825686-56826405	SK-N-SH	brain:	n/a	n/a
23	ATF3	chr19:56825783-56826224	K562	blood:	n/a	chr19:56826006-56826019 chr19:56826009-56826019 chr19:56826005-56826018 chr19:56826006-56826016 chr19:56826008-56826016 chr19:56825997-56826017 chr19:56826009-56826020 chr19:56826009-56826017 chr19:56826009-56826016 chr19:56826008-56826028 chr19:56826006-56826017 chr19:56826009-56826019 chr19:56826006-56826019 chr19:56826005-56826020 chr19:56826007-56826020 chr19:56826008-56826019 chr19:56826007-56826018
24	NR2F2	chr19:56825149-56826236	K562	blood:	n/a	n/a
25	MXI1	chr19:56825660-56826909	H1-hESC	embryonic stem cell:	n/a	chr19:56826864-56826879 chr19:56826866-56826881 chr19:56826045-56826060 chr19:56826043-56826058
26	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
27	ELK4	chr19:56825885-56826804	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr19:56825575-56827068	MCF-7	breast:	n/a	n/a
29	MAZ	chr19:56824862-56827211	IMR90	lung:	n/a	chr19:56826866-56826875 chr19:56826870-56826879 chr19:56826045-56826054
30	BCL3	chr19:56825577-56826649	A549	lung:	n/a	chr19:56826245-56826254 chr19:56826232-56826241
31	ZNF384	chr19:56825611-56826367	K562	blood:	n/a	n/a
32	POLR2A	chr19:56825230-56826966	GM12878	blood:	n/a	n/a
33	PML	chr19:56825455-56826259	K562	blood:	n/a	n/a
34	CCNT2	chr19:56825788-56826236	K562	blood:	n/a	chr19:56826158-56826167
35	ZNF263	chr19:56825406-56826267	K562	blood:	n/a	chr19:56825935-56825944
36	REST	chr19:56825102-56827194	H1-neurons	neurons:	n/a	chr19:56826159-56826172 chr19:56826867-56826876
37	POU2F2	chr19:56825678-56826393	GM12878	blood:	n/a	chr19:56825930-56825942
38	POLR2A	chr19:56825379-56826445	GM12892	blood:	n/a	n/a
39	SRF	chr19:56825833-56826909	MCF-7	breast:	n/a	chr19:56826156-56826166
40	TAF1	chr19:56825410-56826361	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAZ	chr19:56825388-56826421	HepG2	liver:	n/a	chr19:56826045-56826054
42	ELK1	chr19:56825699-56826877	Hela-S3	cervix:	n/a	chr19:56826232-56826241 chr19:56826232-56826241
43	ELF1	chr19:56825669-56826736	A549	lung:	n/a	chr19:56826232-56826243 chr19:56825993-56826005 chr19:56826231-56826244
44	GABPA	chr19:56825690-56826986	MCF-7	breast:	n/a	chr19:56825958-56825972 chr19:56825958-56825967 chr19:56825960-56825969 chr19:56825958-56825969
45	POLR2A	chr19:56825413-56827064	K562	blood:	n/a	n/a
46	MYC	chr19:56825608-56826997	K562	blood:	n/a	chr19:56826866-56826875 chr19:56826870-56826879 chr19:56826045-56826054 chr19:56826599-56826609
47	STAT5A	chr19:56825646-56826235	GM12878	blood:	n/a	chr19:56826159-56826171 chr19:56825706-56825713 chr19:56825968-56825980
48	POLR2A	chr19:56825419-56826971	ProgFib	skin:	n/a	n/a
49	SIN3AK20	chr19:56825579-56826287	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr19:56825578-56826943	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56825335..56828118-chr19:56903219..56906332,4	K562	blood:
2	chr19:56825352..56829856-chr19:56831358..56835885,6	K562	blood:
3	chr19:56824960..56826803-chr19:56913604..56915630,2	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	chr10:99496757..99497468-chr19:56825581..56826247,2	Hela-S3	cervix:
7	chr19:56631391..56633030-chr19:56824712..56827583,2	K562	blood:
8	chr19:56825335..56828118-chr19:56903219..56905060,3	K562	blood:
9	chr19:56631659..56633594-chr19:56825559..56827609,3	MCF-7	breast:
10	chr19:56824639..56829612-chr19:56829732..56835885,11	K562	blood:
11	chr19:56825650..56827475-chr19:56859296..56861906,3	K562	blood:
12	chr19:56825708..56826648-chr6:10722834..10723658,2	Hela-S3	cervix:
13	chr19:56612599..56616950-chr19:56825214..56827593,3	MCF-7	breast:
14	chr19:56825234..56827754-chr19:56833575..56835953,2	MCF-7	breast:
15	chr19:56825808..56826423-chr21:47401255..47401974,2	HCT-116	colon:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF583-5	chr19:56825619-56826355	NONHSAT068099

Variant related genes	Relation type
ZSCAN5A	TF binding region
ENSG00000267298	TF binding region
ENSG00000267549	TF binding region
ENSG00000266907	Chromatin interaction
ENSG00000142156	Chromatin interaction
ENSG00000198440	Chromatin interaction
ENSG00000223060	Chromatin interaction
ENSG00000111843	Chromatin interaction
ENSG00000155256	Chromatin interaction
ENSG00000167685	Chromatin interaction
ENSG00000267429	Chromatin interaction
ENSG00000267454	Chromatin interaction
ENSG00000142409	Chromatin interaction
ENSG00000018869	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11668451	0.80[CEU][hapmap];0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs34008538	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34181036	0.87[EUR][1000 genomes]
rs34709084	0.87[EUR][1000 genomes]
rs34833657	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35366276	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35533663	0.85[EUR][1000 genomes]
rs35560203	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35920556	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60969702	1.00[ASN][1000 genomes]
rs7252814	0.80[CEU][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7253522	0.87[EUR][1000 genomes];1.00[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	chr19:56825400-56826800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:56825400-56826800	Active TSS	Fetal Intestine Large	intestine
21	chr19:56825400-56827000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr19:56825400-56827000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:56825400-56827000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr19:56825400-56827000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr19:56825400-56827000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr19:56825400-56827000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr19:56825400-56827000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:56825400-56827000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr19:56825400-56827000	Active TSS	Aorta	Aorta
30	chr19:56825400-56827000	Active TSS	Brain Substantia Nigra	brain
31	chr19:56825400-56827000	Active TSS	Fetal Intestine Small	intestine
32	chr19:56825400-56827000	Active TSS	Gastric	stomach
33	chr19:56825400-56827000	Active TSS	Right Atrium	heart
34	chr19:56825400-56827000	Active TSS	Sigmoid Colon	Sigmoid Colon
35	chr19:56825400-56827000	Active TSS	Small Intestine	intestine
36	chr19:56825400-56827000	Active TSS	GM12878-XiMat	blood
37	chr19:56825400-56827000	Active TSS	Hela-S3	cervix
38	chr19:56825400-56827000	Active TSS	HSMMtube	muscle
39	chr19:56825400-56827200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr19:56825400-56827200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:56825400-56827200	Active TSS	Ovary	ovary
42	chr19:56825400-56827400	Active TSS	Psoas Muscle	Psoas
43	chr19:56825400-56827400	Active TSS	NHDF-Ad	bronchial
44	chr19:56825400-56827600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr19:56825400-56827600	Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr19:56825400-56827600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr19:56825600-56826000	Active TSS	HepG2	liver
48	chr19:56825600-56826800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:56825600-56826800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr19:56825600-56826800	Active TSS	Primary T cells from cord blood	blood

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