Variant report

Variant	rs525827
Chromosome Location	chr19:56639027-56639028
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	MAX	chr19:56638787-56639178	H1-hESC	embryonic stem cell:	n/a	chr19:56638973-56638983 chr19:56638929-56638939
2	MAX	chr19:56638751-56639137	HepG2	liver:	n/a	chr19:56638973-56638983 chr19:56638929-56638939
3	NFYB	chr19:56638539-56639168	K562	blood:	n/a	chr19:56638912-56638927 chr19:56638862-56638877 chr19:56638863-56638873
4	NFYB	chr19:56638750-56639035	Hela-S3	cervix:	n/a	chr19:56638912-56638927 chr19:56638862-56638877 chr19:56638863-56638873
5	E2F6	chr19:56638824-56639033	K562	blood:	n/a	chr19:56638864-56638873
6	USF1	chr19:56638791-56639031	HepG2	liver:	n/a	chr19:56638929-56638940
7	USF1	chr19:56638778-56639104	A549	lung:	n/a	chr19:56638929-56638940
8	MAX	chr19:56638736-56639241	HepG2	liver:	n/a	chr19:56638973-56638983 chr19:56638929-56638939
9	MAX	chr19:56638749-56639246	ECC-1	luminal epithelium:	n/a	chr19:56638973-56638983 chr19:56638929-56638939
10	USF1	chr19:56638715-56639115	K562	blood:	n/a	chr19:56638929-56638940
11	MAX	chr19:56638739-56639275	H1-hESC	embryonic stem cell:	n/a	chr19:56638973-56638983 chr19:56638929-56638939
12	MYC	chr19:56638860-56639180	K562	blood:	n/a	chr19:56638973-56638983 chr19:56638929-56638939
13	MAX	chr19:56638755-56639207	K562	blood:	n/a	chr19:56638973-56638983 chr19:56638929-56638939
14	USF1	chr19:56638713-56639180	ECC-1	luminal epithelium:	n/a	chr19:56638929-56638940
15	MAX	chr19:56638417-56639152	NB4	blood:	n/a	chr19:56638973-56638983 chr19:56638929-56638939
16	USF2	chr19:56638797-56639120	HepG2	liver:	n/a	n/a
17	USF1	chr19:56638824-56639051	SK-N-SH_RA	brain:	n/a	chr19:56638929-56638940
18	USF2	chr19:56638750-56639115	H1-hESC	embryonic stem cell:	n/a	n/a
19	USF1	chr19:56638747-56639096	H1-hESC	embryonic stem cell:	n/a	chr19:56638929-56638940
20	USF1	chr19:56638793-56639063	A549	lung:	n/a	chr19:56638929-56638940
21	ATF3	chr19:56638803-56639072	K562	blood:	n/a	n/a
22	CBX3	chr19:56638800-56639186	K562	blood:	n/a	n/a
23	NFYA	chr19:56638697-56639174	K562	blood:	n/a	chr19:56638876-56638894 chr19:56638906-56638924 chr19:56638863-56638873
24	MAX	chr19:56638668-56639256	HepG2	liver:	n/a	chr19:56638973-56638983 chr19:56638929-56638939
25	USF1	chr19:56638795-56639050	SK-N-SH	brain:	n/a	chr19:56638929-56638940
26	E2F6	chr19:56638732-56639153	H1-hESC	embryonic stem cell:	n/a	chr19:56638864-56638873
27	USF1	chr19:56638662-56639215	HCT-116	colon:	n/a	chr19:56638929-56638940
28	USF1	chr19:56638832-56639128	ECC-1	luminal epithelium:	n/a	chr19:56638929-56638940
29	USF1	chr19:56638759-56639082	HepG2	liver:	n/a	chr19:56638929-56638940
30	MAX	chr19:56638747-56639217	H1-hESC	embryonic stem cell:	n/a	chr19:56638973-56638983 chr19:56638929-56638939
31	NFYB	chr19:56638748-56639069	GM12878	blood:	n/a	chr19:56638912-56638927 chr19:56638862-56638877 chr19:56638863-56638873
32	USF2	chr19:56638835-56639099	K562	blood:	n/a	n/a
33	USF1	chr19:56638704-56639081	K562	blood:	n/a	chr19:56638929-56638940
34	USF1	chr19:56638664-56639114	H1-hESC	embryonic stem cell:	n/a	chr19:56638929-56638940

No.	Distal block	Cell Line	Cell type
1	chr19:56637204..56640116-chr19:56644041..56647745,4	K562	blood:
2	chr19:56637526..56639987-chr19:56654517..56657150,2	MCF-7	breast:
3	chr19:56638806..56640383-chr19:56686828..56688462,2	K562	blood:
4	chr19:56630485..56634048-chr19:56635782..56640573,5	MCF-7	breast:

Variant related genes	Relation type
ZNF444	TF binding region
ENSG00000167685	Chromatin interaction
ENSG00000197487	Chromatin interaction
ENSG00000142409	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs11673628	0.84[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12459102	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12981138	0.84[ASN][1000 genomes]
rs12983086	0.89[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs2450439	0.96[ASN][1000 genomes]
rs2631625	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2631627	0.95[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2631628	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2631631	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2631637	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2631640	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2637088	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2637092	0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2637094	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2637097	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2637114	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2932757	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs473953	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs478402	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4801676	0.84[CHB][hapmap];0.89[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs481936	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs490345	0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs492078	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs497453	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs501798	0.83[ASN][1000 genomes]
rs504350	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs506547	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs509897	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs517021	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs517582	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs521092	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs522980	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs524778	0.95[ASN][1000 genomes]
rs524829	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs524988	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs527715	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs530102	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs533640	0.83[ASN][1000 genomes]
rs533734	0.83[ASN][1000 genomes]
rs535393	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs536342	0.83[ASN][1000 genomes]
rs536414	0.82[ASN][1000 genomes]
rs537425	0.86[ASN][1000 genomes]
rs540900	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap]
rs544365	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs545570	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs547002	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs547945	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs564050	0.83[ASN][1000 genomes]
rs564973	0.89[ASN][1000 genomes]
rs565879	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs569310	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs572851	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs578990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs578991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs582271	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs583330	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs587702	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs588574	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs592827	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs599405	1.00[CEU][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs609736	0.97[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap]
rs619934	0.83[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs626821	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs628090	0.88[ASN][1000 genomes]
rs629544	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs630704	0.82[ASN][1000 genomes]
rs640654	0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs642776	0.83[AMR][1000 genomes]
rs643133	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs643174	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs659424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs662308	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs662763	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs665082	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs665846	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs665857	0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs667438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs667523	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs667974	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs669866	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs677127	0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs677142	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs678540	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs684653	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs685117	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs8103672	0.84[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs9676765	0.90[JPT][hapmap];0.83[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	nsv1056598	chr19:56331762-56703428	Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv580354	chr19:56505685-56723492	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
5	nsv833883	chr19:56512601-56640089	Strong transcription Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv523651	chr19:56537528-56707048	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
7	nsv1057820	chr19:56555942-56720262	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
8	nsv528998	chr19:56578238-56707048	Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
9	nsv517365	chr19:56592286-56674548	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv912513	chr19:56592286-56685463	Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
11	nsv521744	chr19:56592286-56686953	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
12	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
13	nsv528361	chr19:56638845-56688570	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56633600-56639400	Enhancers	Primary T cells from cord blood	blood
2	chr19:56634000-56640800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr19:56634000-56645400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr19:56636200-56639200	Enhancers	Fetal Muscle Trunk	muscle
5	chr19:56636200-56639200	Enhancers	Fetal Muscle Leg	muscle
6	chr19:56637000-56639200	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr19:56637400-56645400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr19:56637800-56639200	Enhancers	HepG2	liver
9	chr19:56637800-56639200	Enhancers	K562	blood
10	chr19:56637800-56640800	Weak transcription	Fetal Lung	lung
11	chr19:56637800-56643200	Weak transcription	Fetal Stomach	stomach
12	chr19:56637800-56645200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr19:56637800-56647600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:56638600-56643800	Weak transcription	HSMM	muscle
15	chr19:56638600-56643800	Weak transcription	HSMMtube	muscle
16	chr19:56638600-56651200	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr19:56638800-56651800	Weak transcription	Spleen	Spleen
18	chr19:56639000-56647600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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