Variant report

Variant	rs612211
Chromosome Location	chr19:56150471-56150472
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:238)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:238 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PAX5	chr19:56150406-56150756	GM12878	blood:	n/a	n/a
2	CTCF	chr19:56150462-56150710	MCF-7	breast:	n/a	n/a
3	ZNF143	chr19:56150408-56150732	GM12878	blood:	n/a	n/a
4	CTCF	chr19:56150316-56150780	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:56150322-56150821	GM12891	blood:	n/a	n/a
6	POLR2A	chr19:56150319-56156666	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr19:56150176-56150790	GM12878	blood:	n/a	n/a
8	CTCF	chr19:56150427-56150747	A549	lung:	n/a	n/a
9	POLR2A	chr19:56150228-56156269	GM12891	blood:	n/a	n/a
10	MAZ	chr19:56150424-56150630	HepG2	liver:	n/a	n/a
11	USF2	chr19:56150469-56150666	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr19:56150223-56150962	GM12878	blood:	n/a	n/a
13	CEBPB	chr19:56150309-56150683	Hela-S3	cervix:	n/a	n/a
14	FOXA2	chr19:56150316-56150669	A549	lung:	n/a	n/a
15	CTCF	chr19:56150419-56150769	GM12878	blood:	n/a	n/a
16	GABPA	chr19:56150386-56150659	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr19:56150192-56156534	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:56150362-56150642	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr19:56150437-56150657	SK-N-SH	brain:	n/a	n/a
20	MAX	chr19:56150208-56150915	A549	lung:	n/a	n/a
21	CTCF	chr19:56150354-56150807	K562	blood:	n/a	n/a
22	YY1	chr19:56150297-56150741	GM12878	blood:	n/a	chr19:56150495-56150507
23	CTCF	chr19:56150349-56150741	A549	lung:	n/a	n/a
24	MTA3	chr19:56150220-56151043	GM12878	blood:	n/a	n/a
25	MAX	chr19:56150387-56150778	H1-hESC	embryonic stem cell:	n/a	n/a
26	CTCF	chr19:56150467-56150732	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr19:56150380-56151264	Hela-S3	cervix:	n/a	n/a
28	TCF12	chr19:56150454-56150659	H1-hESC	embryonic stem cell:	n/a	n/a
29	CHD1	chr19:56150391-56150750	GM12878	blood:	n/a	n/a
30	POLR2A	chr19:56150393-56150804	Hela-S3	cervix:	n/a	n/a
31	CTCF	chr19:56150420-56150570	HCT-116	colon:	n/a	n/a
32	CTCF	chr19:56150379-56150723	K562	blood:	n/a	n/a
33	CTCF	chr19:56150460-56150610	GM12871	blood:	n/a	n/a
34	RAD21	chr19:56150407-56150729	HepG2	liver:	n/a	n/a
35	YY1	chr19:56150208-56150686	GM12878	blood:	n/a	chr19:56150495-56150507
36	YY1	chr19:56150406-56150752	HepG2	liver:	n/a	chr19:56150495-56150507
37	POLR2A	chr19:56150209-56150972	GM12892	blood:	n/a	n/a
38	ZNF143	chr19:56150426-56150747	Hela-S3	cervix:	n/a	n/a
39	STAT5A	chr19:56150362-56150850	GM12878	blood:	n/a	n/a
40	ZC3H11A	chr19:56150359-56150757	K562	blood:	n/a	n/a
41	MYC	chr19:56150404-56150689	K562	blood:	n/a	n/a
42	TBP	chr19:56150405-56150690	GM12878	blood:	n/a	n/a
43	POLR2A	chr19:56149778-56157300	PANC-1	pancreas:	n/a	n/a
44	RAD21	chr19:56150406-56150704	H1-hESC	embryonic stem cell:	n/a	n/a
45	YY1	chr19:56150350-56150774	GM12892	blood:	n/a	chr19:56150495-56150507
46	YY1	chr19:56150383-56150655	ECC-1	luminal epithelium:	n/a	chr19:56150495-56150507
47	WRNIP1	chr19:56150428-56150644	GM12878	blood:	n/a	n/a
48	CTCF	chr19:56150460-56150610	NHDF-neo	bronchial:	n/a	n/a
49	POLR2A	chr19:56150010-56156634	MCF10A-Er-Src	breast:	n/a	n/a
50	POLR2A	chr19:56148727-56151140	PFSK-1	brain:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:56133203..56138391-chr19:56150309..56156340,8	K562	blood:
2	chr19:56109287..56112853-chr19:56149861..56154883,7	MCF-7	breast:
3	chr19:56115086..56118069-chr19:56150430..56156112,7	MCF-7	breast:
4	chr19:56135345..56138507-chr19:56147845..56151809,4	K562	blood:

No data

Variant related genes	Relation type
ZNF581	TF binding region
ZNF580	TF binding region
CCDC106	TF binding region
ENSG00000171443	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000261221	Chromatin interaction
ENSG00000179943	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs310464	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs310465	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs310467	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs310470	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310471	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs310474	0.89[EUR][1000 genomes]
rs504003	1.00[CHB][hapmap]
rs507498	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs520125	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs522669	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs553947	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs581023	0.84[EUR][1000 genomes]
rs636466	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs636467	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs637788	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[EUR][1000 genomes]
rs644230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681433	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs7246799	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7251872	0.86[ASN][1000 genomes]
rs7259701	1.00[MEX][hapmap]
rs889091	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	nsv428026	chr19:56130849-56423514	Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	82 gene(s)	inside rSNPs	diseases
8	nsv912503	chr19:56149077-56162776	Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
9	nsv912504	chr19:56149077-56170415	Flanking Active TSS Genic enhancers Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56147800-56151400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:56147800-56151400	Enhancers	Liver	Liver
3	chr19:56147800-56151400	Enhancers	Brain Substantia Nigra	brain
4	chr19:56147800-56151600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr19:56147800-56151600	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr19:56147800-56151600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr19:56147800-56151600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr19:56147800-56151600	Weak transcription	Fetal Heart	heart
9	chr19:56147800-56151600	Enhancers	Pancreas	Pancrea
10	chr19:56147800-56151800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:56147800-56151800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr19:56148000-56150600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr19:56148000-56150800	Weak transcription	Fetal Kidney	kidney
14	chr19:56148000-56151400	Enhancers	Duodenum Smooth Muscle	Duodenum
15	chr19:56148200-56150600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:56148200-56150600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr19:56148200-56150600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr19:56148200-56151000	Weak transcription	Stomach Mucosa	stomach
19	chr19:56148200-56151200	Weak transcription	Small Intestine	intestine
20	chr19:56148200-56151200	Weak transcription	HUVEC	blood vessel
21	chr19:56148200-56151400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:56148200-56151400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr19:56148200-56151400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr19:56148200-56151400	Weak transcription	HMEC	breast
25	chr19:56148200-56151400	Weak transcription	HSMM	muscle
26	chr19:56148200-56151400	Weak transcription	HSMMtube	muscle
27	chr19:56148200-56151400	Weak transcription	NHEK	skin
28	chr19:56148200-56151600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr19:56148200-56151600	Enhancers	Adipose Nuclei	Adipose
30	chr19:56148200-56151800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr19:56148200-56151800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:56148400-56150600	Weak transcription	Right Atrium	heart
33	chr19:56148400-56150600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr19:56148400-56151200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr19:56148400-56151200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr19:56148400-56151200	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr19:56148400-56151200	Weak transcription	Colonic Mucosa	Colon
38	chr19:56148400-56151200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr19:56148400-56151200	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr19:56148400-56151200	Weak transcription	NH-A	brain
41	chr19:56148400-56151200	Weak transcription	Osteobl	bone
42	chr19:56148400-56151400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:56148400-56151400	Weak transcription	Brain Anterior Caudate	brain
44	chr19:56148400-56151400	Weak transcription	Esophagus	oesophagus
45	chr19:56148400-56151400	Weak transcription	Fetal Lung	lung
46	chr19:56148400-56151400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr19:56148400-56151400	Enhancers	Dnd41	blood
48	chr19:56148400-56151400	Weak transcription	NHLF	lung
49	chr19:56148600-56150800	Enhancers	GM12878-XiMat	blood
50	chr19:56149000-56151200	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links