Variant report

Variant	rs2904016
Chromosome Location	chr19:56904151-56904152
allele	G/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	CEBPB	chr19:56904113-56904448	A549	lung:	n/a	chr19:56904265-56904276 chr19:56904254-56904265
2	CEBPB	chr19:56904087-56904443	K562	blood:	n/a	chr19:56904265-56904276 chr19:56904254-56904265
3	CEBPB	chr19:56904082-56904430	IMR90	lung:	n/a	chr19:56904265-56904276 chr19:56904254-56904265
4	CTCF	chr19:56903940-56905833	SK-N-SH	brain:	n/a	chr19:56904906-56904919 chr19:56904904-56904920 chr19:56904905-56904926 chr19:56904903-56904921 chr19:56904846-56904859
5	CEBPB	chr19:56904104-56904389	HepG2	liver:	n/a	chr19:56904265-56904276 chr19:56904254-56904265
6	POLR2A	chr19:56903999-56904382	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:56878056..56881655-chr19:56903333..56906269,5	K562	blood:
2	chr19:56630391..56632820-chr19:56902199..56906311,3	K562	blood:
3	chr19:56896992..56902951-chr19:56903012..56907037,12	K562	blood:
4	chr19:56902006..56908060-chr19:56909612..56917978,15	K562	blood:
5	chr19:56878151..56881655-chr19:56903333..56906269,7	K562	blood:
6	chr19:56895475..56897823-chr19:56903707..56905886,2	K562	blood:
7	chr19:56825335..56828118-chr19:56903219..56906332,4	K562	blood:
8	chr19:56630391..56632820-chr19:56902199..56904998,2	K562	blood:
9	chr19:56825335..56828118-chr19:56903219..56905060,3	K562	blood:
10	chr19:56902257..56906485-chr19:56913118..56917978,7	K562	blood:
11	chr19:56886550..56889123-chr19:56903257..56905976,3	K562	blood:

Variant related genes	Relation type
ZNF582-AS1	TF binding region
ENSG00000267776	Chromatin interaction
ENSG00000131848	Chromatin interaction
ENSG00000267606	Chromatin interaction
ENSG00000142409	Chromatin interaction
ENSG00000267549	Chromatin interaction
ENSG00000200646	Chromatin interaction
ENSG00000198440	Chromatin interaction
ENSG00000267192	Chromatin interaction
ENSG00000267781	Chromatin interaction
ENSG00000240225	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10408604	0.96[CEU][hapmap]
rs10415307	1.00[CEU][hapmap]
rs10416345	0.96[CEU][hapmap]
rs10419332	0.96[CEU][hapmap]
rs10421407	0.88[CEU][hapmap]
rs10432288	0.83[EUR][1000 genomes]
rs11084446	0.87[EUR][1000 genomes]
rs11084449	0.83[EUR][1000 genomes]
rs11084450	0.85[EUR][1000 genomes]
rs11667815	0.81[EUR][1000 genomes]
rs12460342	0.85[EUR][1000 genomes]
rs12608966	0.87[EUR][1000 genomes]
rs12609819	0.83[EUR][1000 genomes]
rs12610115	0.89[EUR][1000 genomes]
rs12973407	0.93[CEU][hapmap];0.86[EUR][1000 genomes]
rs12981146	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs12981443	0.86[EUR][1000 genomes]
rs2288860	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28373215	0.84[EUR][1000 genomes]
rs2904017	0.85[EUR][1000 genomes]
rs35914474	0.81[EUR][1000 genomes]
rs3745826	0.82[EUR][1000 genomes]
rs3760849	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs3810340	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs4281830	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs4801163	0.88[CEU][hapmap]
rs4801319	0.84[EUR][1000 genomes]
rs56301546	0.90[EUR][1000 genomes]
rs59858465	0.90[EUR][1000 genomes]
rs62121590	0.81[EUR][1000 genomes]
rs7248278	0.84[EUR][1000 genomes]
rs7252607	0.86[EUR][1000 genomes]
rs7258010	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs728232	0.85[EUR][1000 genomes]
rs8102580	0.81[EUR][1000 genomes]
rs8104319	0.85[EUR][1000 genomes]
rs8104585	0.85[EUR][1000 genomes]
rs8112531	0.81[EUR][1000 genomes]
rs8112935	0.81[EUR][1000 genomes]
rs917650	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs917651	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs917652	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs9304776	0.88[CEU][hapmap]
rs9749140	0.82[EUR][1000 genomes]
rs9789281	0.86[EUR][1000 genomes]

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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2904016	ZNF582-AS1	cis	Adipose Subcutaneous	GTEx
rs2904016	ZNF582-AS1	cis	Artery Tibial	GTEx
rs2904016	ZNF582-AS1	cis	Esophagus Muscularis	GTEx
rs2904016	ZNF582-AS1	cis	lung	GTEx

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56889200-56904400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr19:56896000-56904400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr19:56896600-56904200	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr19:56897400-56904200	Weak transcription	NHLF	lung
5	chr19:56898200-56904200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr19:56899400-56904200	Weak transcription	NH-A	brain
7	chr19:56900000-56906800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr19:56900800-56904400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:56900800-56904400	Weak transcription	HSMMtube	muscle
10	chr19:56901400-56904200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr19:56901600-56904600	Weak transcription	Small Intestine	intestine
12	chr19:56901800-56904200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:56901800-56904200	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr19:56901800-56904200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr19:56901800-56904200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr19:56901800-56904200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:56901800-56904400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:56901800-56904600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr19:56902000-56904200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr19:56902000-56904200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr19:56902000-56904200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:56902000-56904200	Weak transcription	Aorta	Aorta
23	chr19:56902000-56904400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:56902000-56904400	Weak transcription	Colonic Mucosa	Colon
25	chr19:56902000-56904400	Weak transcription	Esophagus	oesophagus
26	chr19:56902000-56904400	Weak transcription	Placenta	Placenta
27	chr19:56902000-56904400	Weak transcription	Thymus	Thymus
28	chr19:56902000-56904600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr19:56902000-56904600	Weak transcription	Pancreas	Pancrea
30	chr19:56902200-56904200	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:56902200-56904200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:56902200-56904200	Weak transcription	Brain Germinal Matrix	brain
33	chr19:56902200-56904200	Weak transcription	Fetal Brain Female	brain
34	chr19:56902200-56904200	Weak transcription	Fetal Intestine Large	intestine
35	chr19:56902200-56904400	Weak transcription	HSMM	muscle
36	chr19:56902400-56904200	Weak transcription	Stomach Mucosa	stomach
37	chr19:56902600-56904200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr19:56902800-56904200	Weak transcription	Primary B cells from peripheral blood	blood
39	chr19:56902800-56904400	Weak transcription	Fetal Muscle Trunk	muscle
40	chr19:56903000-56904200	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr19:56903000-56904400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr19:56903200-56904200	Weak transcription	Primary B cells from cord blood	blood
43	chr19:56903400-56904200	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr19:56903400-56904200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr19:56903400-56904200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr19:56903400-56904200	Weak transcription	Fetal Stomach	stomach
47	chr19:56903400-56905200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:56903400-56906000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr19:56903600-56904200	Enhancers	Primary T helper cells PMA-I stimulated	--
50	chr19:56903600-56904200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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