Variant report

Variant	rs497264
Chromosome Location	chr19:56109916-56109917
allele	A/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	POLR2A	chr19:56109885-56109946	HepG2	liver:	n/a	n/a
2	REST	chr19:56109773-56111723	A549	lung:	n/a	chr19:56110729-56110742 chr19:56110666-56110679 chr19:56111112-56111120 chr19:56110867-56110880
3	RCOR1	chr19:56109857-56110127	K562	blood:	n/a	n/a
4	SIX5	chr19:56109803-56111779	A549	lung:	n/a	chr19:56110837-56110846
5	BCL3	chr19:56109863-56111604	A549	lung:	n/a	chr19:56110549-56110558 chr19:56110866-56110879 chr19:56110667-56110680 chr19:56110804-56110813 chr19:56111056-56111069
6	TCF12	chr19:56109655-56112962	A549	lung:	n/a	n/a
7	MAFK	chr19:56109857-56109954	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:56109899-56111645	K562	blood:	n/a	n/a
9	POLR2A	chr19:56109904-56111701	HepG2	liver:	n/a	n/a
10	RELA	chr19:56109849-56112349	GM12891	blood:	n/a	n/a
11	GATA3	chr19:56109853-56111855	A549	lung:	n/a	chr19:56111599-56111609 chr19:56110027-56110037
12	MAZ	chr19:56109801-56112631	IMR90	lung:	n/a	chr19:56111783-56111793 chr19:56110495-56110505
13	MXI1	chr19:56109904-56110009	H1-hESC	embryonic stem cell:	n/a	n/a
14	MYC	chr19:56109887-56111680	H1-hESC	embryonic stem cell:	n/a	chr19:56110495-56110505

No.	Distal block	Cell Line	Cell type
1	chr19:55986000..55989537-chr19:56108522..56112833,7	MCF-7	breast:
2	chr19:56109729..56112451-chr19:56165377..56168122,5	MCF-7	breast:
3	chr19:56046531..56048112-chr19:56108698..56111511,2	MCF-7	breast:
4	chr19:55986419..55989388-chr19:56109213..56112341,4	K562	blood:
5	chr19:55994299..55997215-chr19:56109132..56111964,3	K562	blood:
6	chr19:55917748..55920668-chr19:56108970..56111070,3	K562	blood:
7	chr19:56109380..56112832-chr19:56163189..56166704,4	K562	blood:
8	chr19:55917650..55919623-chr19:56109574..56112521,4	MCF-7	breast:
9	chr19:56109378..56114662-chr19:56134412..56139001,15	K562	blood:
10	chr19:56087311..56094258-chr19:56108819..56113699,11	K562	blood:
11	chr19:56109576..56111086-chr19:56151064..56152602,2	K562	blood:
12	chr19:56087628..56093963-chr19:56108517..56113906,9	MCF-7	breast:
13	chr19:56109287..56112853-chr19:56149861..56154883,7	MCF-7	breast:
14	chr19:56091409..56094452-chr19:56108819..56113428,6	K562	blood:
15	chr19:56107792..56111497-chr19:56151607..56154571,3	MCF-7	breast:

Variant related genes	Relation type
FIZ1	TF binding region
ZNF524	TF binding region
ENSG00000197483	Chromatin interaction
ENSG00000063244	Chromatin interaction
ENSG00000187550	Chromatin interaction
ENSG00000218891	Chromatin interaction
ENSG00000267730	Chromatin interaction
ENSG00000173581	Chromatin interaction
ENSG00000213015	Chromatin interaction
ENSG00000171425	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000090971	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000108106	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1423053	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1423054	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs2902749	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs310458	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs310459	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs310460	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs310461	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs310462	0.90[ASN][1000 genomes]
rs498199	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs609075	1.00[CEU][hapmap];0.82[CHB][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912473	chr19:55874642-56145428	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
2	nsv912486	chr19:55977909-56145428	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv912487	chr19:55977909-56215184	Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv912494	chr19:56026072-56215184	Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
5	nsv912495	chr19:56033088-56132661	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
6	nsv912496	chr19:56040051-56145428	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv912497	chr19:56041848-56145428	Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
8	nsv912498	chr19:56041848-56215184	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
9	nsv828643	chr19:56059280-56154823	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
10	nsv912499	chr19:56071293-56132487	Flanking Active TSS Genic enhancers Active TSS Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
11	nsv912500	chr19:56078722-56175515	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	86 gene(s)	inside rSNPs	diseases
12	nsv912501	chr19:56093365-56215184	Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
13	nsv912502	chr19:56099884-56138575	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs497264	ZNF444	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56099200-56110000	Weak transcription	Right Atrium	heart
2	chr19:56099800-56110000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr19:56099800-56110400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr19:56102800-56110600	Weak transcription	Stomach Mucosa	stomach
5	chr19:56104800-56110000	Strong transcription	NHEK	skin
6	chr19:56105200-56110400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr19:56107000-56110400	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr19:56107200-56110600	Weak transcription	Small Intestine	intestine
9	chr19:56107800-56110000	Weak transcription	Fetal Brain Male	brain
10	chr19:56107800-56110200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr19:56107800-56110200	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr19:56107800-56110400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr19:56108000-56110000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr19:56108000-56110000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr19:56108000-56110000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr19:56108000-56110000	Weak transcription	Brain Angular Gyrus	brain
17	chr19:56108000-56110000	Weak transcription	Brain Hippocampus Middle	brain
18	chr19:56108000-56110000	Weak transcription	Psoas Muscle	Psoas
19	chr19:56108000-56110000	Weak transcription	HMEC	breast
20	chr19:56108000-56110000	Weak transcription	HSMM	muscle
21	chr19:56108000-56110200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr19:56108000-56110400	Weak transcription	Colonic Mucosa	Colon
23	chr19:56108000-56110400	Weak transcription	Esophagus	oesophagus
24	chr19:56108000-56110600	Weak transcription	Aorta	Aorta
25	chr19:56108200-56110000	Weak transcription	Fetal Kidney	kidney
26	chr19:56108200-56110200	Weak transcription	Osteobl	bone
27	chr19:56108600-56110000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr19:56108600-56110000	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr19:56108800-56110000	Weak transcription	Primary B cells from peripheral blood	blood
30	chr19:56108800-56110000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr19:56108800-56110000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr19:56108800-56110000	Weak transcription	HSMMtube	muscle
33	chr19:56108800-56110400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr19:56108800-56111600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr19:56109000-56110000	Weak transcription	Primary B cells from cord blood	blood
36	chr19:56109000-56110000	Weak transcription	Primary T cells from cord blood	blood
37	chr19:56109000-56110000	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr19:56109000-56110000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr19:56109000-56110000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr19:56109000-56110000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr19:56109000-56110200	Weak transcription	Placenta	Placenta
42	chr19:56109000-56110200	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr19:56109000-56110200	Weak transcription	Monocytes-CD14+_RO01746	blood
44	chr19:56109000-56110400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr19:56109000-56110600	Weak transcription	Ovary	ovary
46	chr19:56109000-56112400	Active TSS	H9 Cell Line	embryonic stem cell
47	chr19:56109200-56110000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr19:56109200-56110000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr19:56109200-56110000	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr19:56109200-56110000	Weak transcription	Liver	Liver

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