Variant report

Variant	rs60799292
Chromosome Location	chr19:55678713-55678714
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	CEBPB	chr19:55678238-55678843	K562	blood:	n/a	chr19:55678315-55678332
2	CEBPB	chr19:55678489-55678713	K562	blood:	n/a	n/a
3	NRF1	chr19:55678250-55678768	K562	blood:	n/a	chr19:55678577-55678588
4	RCOR1	chr19:55677348-55679357	Hela-S3	cervix:	n/a	n/a
5	HA-E2F1	chr19:55678091-55678975	MCF-7	breast:	n/a	chr19:55678165-55678174
6	TCF7L2	chr19:55677370-55678721	HCT-116	colon:	n/a	n/a
7	MAX	chr19:55677266-55678748	A549	lung:	n/a	n/a
8	NRF1	chr19:55677983-55678760	Hela-S3	cervix:	n/a	chr19:55678577-55678588
9	POLR2A	chr19:55677743-55678902	SK-N-MC	brain:	n/a	n/a
10	MAX	chr19:55677114-55678906	A549	lung:	n/a	n/a
11	CEBPB	chr19:55678107-55678906	A549	lung:	n/a	chr19:55678315-55678332
12	SP1	chr19:55677194-55678829	A549	lung:	n/a	chr19:55678402-55678411 chr19:55678402-55678411 chr19:55677857-55677864 chr19:55678197-55678208 chr19:55678041-55678062 chr19:55678082-55678103 chr19:55678403-55678412 chr19:55678176-55678187 chr19:55677824-55677838
13	NRF1	chr19:55677945-55678876	SK-N-SH	brain:	n/a	chr19:55678577-55678588
14	TCF12	chr19:55677159-55678932	A549	lung:	n/a	n/a
15	SREBP1	chr19:55677827-55678813	GM12878	blood:	n/a	chr19:55678147-55678161 chr19:55678148-55678162
16	POLR2A	chr19:55678069-55678837	PANC-1	pancreas:	n/a	n/a
17	SMARCC2	chr19:55678145-55679382	Hela-S3	cervix:	n/a	n/a
18	MAX	chr19:55677270-55678800	MCF-7	breast:	n/a	n/a
19	CTCF	chr19:55676755-55678947	A549	lung:	n/a	chr19:55677561-55677574
20	SIX5	chr19:55677007-55678888	A549	lung:	n/a	chr19:55677447-55677456 chr19:55677445-55677454
21	REST	chr19:55677879-55678723	A549	lung:	n/a	chr19:55678398-55678408
22	TCF7L2	chr19:55677969-55678803	Hela-S3	cervix:	n/a	n/a
23	SIN3AK20	chr19:55677126-55678953	MCF-7	breast:	n/a	n/a
24	CEBPB	chr19:55678403-55678795	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr19:55677788-55678763	H1-neurons	neurons:	n/a	n/a
26	CEBPB	chr19:55678385-55678839	A549	lung:	n/a	n/a
27	GATA3	chr19:55677357-55678857	A549	lung:	n/a	n/a
28	BRCA1	chr19:55677896-55678759	Hela-S3	cervix:	n/a	n/a
29	MAX	chr19:55677736-55678905	ECC-1	luminal epithelium:	n/a	n/a
30	EP300	chr19:55677431-55678803	ECC-1	luminal epithelium:	n/a	chr19:55678279-55678293 chr19:55678161-55678170 chr19:55677546-55677562 chr19:55678398-55678414
31	FOSL2	chr19:55677135-55678731	A549	lung:	n/a	chr19:55677826-55677835 chr19:55678397-55678406 chr19:55678085-55678094 chr19:55677821-55677830 chr19:55678251-55678263 chr19:55678044-55678053
32	TBP	chr19:55678019-55678741	Hela-S3	cervix:	n/a	n/a
33	ATF3	chr19:55678071-55678868	A549	lung:	n/a	n/a
34	SP1	chr19:55677146-55678861	HCT-116	colon:	n/a	chr19:55678402-55678411 chr19:55678402-55678411 chr19:55677857-55677864 chr19:55678197-55678208 chr19:55678041-55678062 chr19:55678082-55678103 chr19:55678403-55678412 chr19:55678176-55678187 chr19:55677824-55677838
35	MAX	chr19:55677365-55678894	Hela-S3	cervix:	n/a	n/a
36	BCL3	chr19:55677972-55678802	A549	lung:	n/a	n/a
37	SP1	chr19:55677151-55678820	A549	lung:	n/a	chr19:55678402-55678411 chr19:55678402-55678411 chr19:55677857-55677864 chr19:55678197-55678208 chr19:55678041-55678062 chr19:55678082-55678103 chr19:55678403-55678412 chr19:55678176-55678187 chr19:55677824-55677838
38	JUND	chr19:55677104-55678848	SK-N-SH	brain:	n/a	chr19:55677826-55677835 chr19:55678397-55678406 chr19:55678085-55678094 chr19:55677821-55677830 chr19:55678251-55678263 chr19:55678044-55678053
39	MAX	chr19:55677405-55679241	Hela-S3	cervix:	n/a	n/a
40	SMC3	chr19:55677369-55679284	Hela-S3	cervix:	n/a	chr19:55677561-55677575
41	HCFC1	chr19:55676917-55678968	Hela-S3	cervix:	n/a	n/a
42	MAX	chr19:55677823-55678750	ECC-1	luminal epithelium:	n/a	n/a
43	CEBPB	chr19:55678153-55678885	K562	blood:	n/a	chr19:55678315-55678332
44	POLR2A	chr19:55677219-55678971	K562	blood:	n/a	n/a
45	SIN3AK20	chr19:55677961-55678842	A549	lung:	n/a	n/a
46	CEBPB	chr19:55678366-55678886	MCF-7	breast:	n/a	n/a
47	CEBPB	chr19:55678431-55678774	HepG2	liver:	n/a	n/a
48	POLR2A	chr19:55678280-55678809	HCT-116	colon:	n/a	n/a
49	CEBPB	chr19:55678237-55678954	A549	lung:	n/a	chr19:55678315-55678332
50	SIN3AK20	chr19:55677327-55678722	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:55678413..55680663-chr19:55987630..55990002,2	MCF-7	breast:
2	chr19:55670803..55672973-chr19:55678461..55680015,2	MCF-7	breast:
3	chr19:55676623..55678727-chr19:55917591..55919258,2	MCF-7	breast:
4	chr19:55677411..55679148-chr19:55895317..55896952,2	MCF-7	breast:
5	chr19:55677572..55679137-chr19:55970708..55972707,2	K562	blood:
6	chr19:55676191..55679387-chr19:55917452..55919839,3	K562	blood:
7	chr19:55676374..55679520-chr19:55726674..55730754,4	K562	blood:
8	chr19:55592134..55595044-chr19:55674815..55678963,4	K562	blood:
9	chr19:55672196..55674741-chr19:55676544..55679173,3	K562	blood:
10	chr19:55677235..55679036-chr19:55897209..55898733,2	K562	blood:
11	chr19:55677803..55679380-chr19:55684043..55686956,2	MCF-7	breast:
12	chr19:55677887..55680823-chr19:55918139..55920221,3	K562	blood:
13	chr19:55590129..55594149-chr19:55677127..55678963,3	K562	blood:

Variant related genes	Relation type
DNAAF3	TF binding region
ENSG00000233493	Chromatin interaction
ENSG00000269859	Chromatin interaction
ENSG00000129990	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000108107	Chromatin interaction
ENSG00000063241	Chromatin interaction
ENSG00000267649	Chromatin interaction
ENSG00000131037	Chromatin interaction
ENSG00000197483	Chromatin interaction
ENSG00000167646	Chromatin interaction
ENSG00000267110	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10421953	0.84[ASN][1000 genomes]
rs10423713	0.85[ASN][1000 genomes]
rs1128712	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12459688	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12459887	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12459917	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12459921	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12459930	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12460445	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12461148	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12461170	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12461195	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12461202	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12462211	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12463268	0.80[AMR][1000 genomes]
rs17458	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2071572	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2071574	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2278281	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2288420	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2288528	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2288529	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2301278	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3745922	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3786867	0.97[ASN][1000 genomes]
rs3826887	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3848618	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3859544	0.95[ASN][1000 genomes]
rs56666700	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56726774	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58017412	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58218194	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58824375	1.00[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs59663064	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60176657	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61570139	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7255625	0.98[ASN][1000 genomes]
rs890871	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9710458	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534462	chr19:55028722-55683018	Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv912451	chr19:55595687-55680746	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv912453	chr19:55672007-55690398	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:55677200-55678800	Active TSS	iPS-15b Cell Line	embryonic stem cell
2	chr19:55677200-55678800	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
3	chr19:55677200-55679000	Enhancers	Spleen	Spleen
4	chr19:55677200-55679200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
5	chr19:55677400-55678800	Active TSS	HUES64 Cell Line	embryonic stem cell
6	chr19:55677400-55678800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr19:55677400-55678800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
8	chr19:55677400-55678800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr19:55677400-55678800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
10	chr19:55677400-55678800	Bivalent/Poised TSS	Duodenum Mucosa	Duodenum
11	chr19:55677400-55678800	Active TSS	Fetal Kidney	kidney
12	chr19:55677400-55678800	Active TSS	NHDF-Ad	bronchial
13	chr19:55677400-55679000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
14	chr19:55677400-55679000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
15	chr19:55677400-55679000	Active TSS	A549	lung
16	chr19:55677400-55679200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
17	chr19:55677600-55678800	Active TSS	H9 Cell Line	embryonic stem cell
18	chr19:55677600-55678800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:55677600-55678800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr19:55677600-55678800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:55677600-55678800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr19:55677600-55678800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
23	chr19:55677600-55678800	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:55677600-55678800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
25	chr19:55677600-55678800	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr19:55677600-55679000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr19:55677600-55679000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr19:55677600-55679200	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
29	chr19:55677600-55679200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr19:55677800-55678800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
31	chr19:55677800-55678800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr19:55677800-55679000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:55677800-55679000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr19:55677800-55679000	Active TSS	Right Ventricle	heart
35	chr19:55678000-55678800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr19:55678000-55678800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:55678000-55678800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
38	chr19:55678000-55678800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
39	chr19:55678000-55679000	Enhancers	Pancreas	Pancrea
40	chr19:55678000-55679200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr19:55678000-55679200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
42	chr19:55678200-55678800	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
43	chr19:55678200-55678800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr19:55678200-55678800	Flanking Active TSS	HMEC	breast
45	chr19:55678200-55679000	Weak transcription	Esophagus	oesophagus
46	chr19:55678200-55679000	Bivalent Enhancer	Placenta	Placenta
47	chr19:55678200-55679200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
48	chr19:55678200-55679200	Flanking Active TSS	NHEK	skin
49	chr19:55678200-55679400	Flanking Active TSS	Hela-S3	cervix
50	chr19:55678400-55678800	Flanking Active TSS	H1 Cell Line	embryonic stem cell

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