Variant report

Variant	rs61288778
Chromosome Location	chr19:40042473-40042474
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	RAD21	chr19:40041989-40042503	H1-hESC	embryonic stem cell:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
2	CTCF	chr19:40041989-40042497	A549	lung:	n/a	chr19:40042250-40042268 chr19:40042255-40042263 chr19:40042253-40042266 chr19:40042252-40042273
3	GATA3	chr19:40042120-40042487	SK-N-SH	brain:	n/a	chr19:40042328-40042336
4	RAD21	chr19:40042092-40042529	ECC-1	luminal epithelium:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
5	CTCF	chr19:40041878-40043166	A549	lung:	n/a	chr19:40042250-40042268 chr19:40042255-40042263 chr19:40042253-40042266 chr19:40042252-40042273
6	REST	chr19:40041997-40043353	PANC-1	pancreas:	n/a	n/a
7	RAD21	chr19:40042056-40042503	HepG2	liver:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
8	RAD21	chr19:40041992-40042624	HCT-116	colon:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
9	CTCF	chr19:40042077-40042529	MCF-7	breast:	n/a	chr19:40042250-40042268 chr19:40042255-40042263 chr19:40042253-40042266 chr19:40042252-40042273
10	FOXM1	chr19:40042051-40042672	GM12878	blood:	n/a	n/a
11	CTCF	chr19:40042034-40042625	SK-N-SH	brain:	n/a	chr19:40042250-40042268 chr19:40042255-40042263 chr19:40042253-40042266 chr19:40042252-40042273
12	RAD21	chr19:40042129-40042540	HCT-116	colon:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
13	CTCF	chr19:40042047-40042535	K562	blood:	n/a	chr19:40042250-40042268 chr19:40042255-40042263 chr19:40042253-40042266 chr19:40042252-40042273
14	RAD21	chr19:40042065-40042716	SK-N-SH	brain:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
15	CTCF	chr19:40042071-40042543	HCT-116	colon:	n/a	chr19:40042250-40042268 chr19:40042255-40042263 chr19:40042253-40042266 chr19:40042252-40042273
16	MTA3	chr19:40042032-40042654	GM12878	blood:	n/a	n/a
17	RAD21	chr19:40042003-40042568	MCF-7	breast:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
18	RAD21	chr19:40042087-40042482	SK-N-SH_RA	brain:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
19	RAD21	chr19:40042083-40042494	A549	lung:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
20	SMC3	chr19:40042063-40042505	GM12878	blood:	n/a	chr19:40042252-40042266
21	ZNF384	chr19:40042104-40042540	GM12878	blood:	n/a	n/a
22	RAD21	chr19:40042049-40042590	A549	lung:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
23	SMC3	chr19:40042051-40042625	SK-N-SH	brain:	n/a	chr19:40042252-40042266
24	CTCF	chr19:40042127-40042498	MCF-7	breast:	n/a	chr19:40042250-40042268 chr19:40042255-40042263 chr19:40042253-40042266 chr19:40042252-40042273
25	RAD21	chr19:40041991-40042615	H1-hESC	embryonic stem cell:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
26	CTCF	chr19:40042063-40042476	K562	blood:	n/a	chr19:40042250-40042268 chr19:40042255-40042263 chr19:40042253-40042266 chr19:40042252-40042273
27	RAD21	chr19:40042036-40042609	MCF-7	breast:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
28	CTCF	chr19:40042040-40042478	A549	lung:	n/a	chr19:40042250-40042268 chr19:40042255-40042263 chr19:40042253-40042266 chr19:40042252-40042273
29	RAD21	chr19:40042008-40042542	ECC-1	luminal epithelium:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
30	RAD21	chr19:40042086-40042477	GM12878	blood:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
31	RAD21	chr19:40042018-40042569	A549	lung:	n/a	chr19:40042256-40042268 chr19:40042255-40042264 chr19:40042251-40042270 chr19:40042253-40042260 chr19:40042254-40042267
32	GATA2	chr19:40042150-40042523	HUVEC	blood vessel:	n/a	chr19:40042328-40042336

No.	Distal block	Cell Line	Cell type
1	chr19:40041791..40042737-chr19:40118062..40118973,2	MCF-7	breast:
2	chr19:40041798..40042719-chr19:40162291..40163385,9	MCF-7	breast:
3	chr19:40041783..40042891-chr19:40162333..40163330,4	K562	blood:
4	chr19:40041769..40042752-chr19:40257039..40257543,2	K562	blood:
5	chr19:40041871..40042653-chr19:40162390..40162892,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269588	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10403625	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10403763	0.96[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10407315	0.91[AMR][1000 genomes]
rs10415807	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10418049	0.91[AMR][1000 genomes]
rs10426230	0.95[AMR][1000 genomes]
rs1433109	0.90[EUR][1000 genomes]
rs16973498	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2010106	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2082483	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57386718	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57484954	0.90[EUR][1000 genomes]
rs57713278	0.90[EUR][1000 genomes]
rs58916238	0.90[EUR][1000 genomes]
rs7248055	0.90[EUR][1000 genomes]
rs72480723	0.90[EUR][1000 genomes]
rs72480724	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7251429	0.86[EUR][1000 genomes]
rs7255034	0.90[EUR][1000 genomes]
rs7260569	0.86[EUR][1000 genomes]
rs73930747	0.90[EUR][1000 genomes]
rs8100675	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8101913	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8108805	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911690	chr19:39903088-40046863	Weak transcription Bivalent Enhancer Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv911692	chr19:39979966-40046863	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1060251	chr19:39982988-40099773	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
4	nsv579509	chr19:40004640-40133438	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40031200-40043600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr19:40031200-40049600	Weak transcription	Right Atrium	heart
3	chr19:40038600-40048000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr19:40041200-40048200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr19:40042000-40042600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
6	chr19:40042000-40043600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr19:40042200-40042800	Enhancers	Placenta	Placenta
8	chr19:40042200-40043200	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr19:40042200-40043800	Enhancers	Primary hematopoietic stem cells	blood
10	chr19:40042200-40044000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr19:40042200-40044200	Enhancers	Primary B cells from cord blood	blood
12	chr19:40042200-40044200	Enhancers	Primary B cells from peripheral blood	blood
13	chr19:40042200-40044200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr19:40042200-40047200	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr19:40042400-40042600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr19:40042400-40042800	Flanking Active TSS	GM12878-XiMat	blood
17	chr19:40042400-40043000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr19:40042400-40043000	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr19:40042400-40043000	Enhancers	Adipose Nuclei	Adipose
20	chr19:40042400-40043000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr19:40042400-40043200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr19:40042400-40043800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr19:40042400-40044200	Enhancers	Spleen	Spleen

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