Variant report

Variant	rs12979133
Chromosome Location	chr19:52098208-52098209
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	BCL3	chr19:52097374-52098262	A549	lung:	n/a	chr19:52097706-52097719 chr19:52097907-52097920
2	NRF1	chr19:52096917-52098423	SK-N-SH	brain:	n/a	chr19:52097639-52097648 chr19:52097639-52097653 chr19:52097639-52097650 chr19:52097636-52097650 chr19:52097644-52097655
3	HCFC1	chr19:52097053-52098362	Hela-S3	cervix:	n/a	n/a
4	SETDB1	chr19:52097506-52098248	K562	blood:	n/a	chr19:52097640-52097649 chr19:52097718-52097742 chr19:52097818-52097842
5	POLR2A	chr19:52095947-52098295	K562	blood:	n/a	n/a
6	MAX	chr19:52097217-52098234	K562	blood:	n/a	n/a
7	ZNF263	chr19:52096973-52098574	HEK293-T-REx	kidney:	n/a	n/a
8	CHD2	chr19:52097118-52098214	K562	blood:	n/a	n/a
9	ZNF143	chr19:52097417-52098249	K562	blood:	n/a	chr19:52097822-52097840 chr19:52097729-52097738 chr19:52097722-52097740 chr19:52097831-52097840 chr19:52097789-52097807 chr19:52097796-52097805 chr19:52097829-52097838
10	MYC	chr19:52097472-52098336	K562	blood:	n/a	n/a
11	CTCF	chr19:52098100-52098250	GM12873	blood:	n/a	n/a
12	ELF1	chr19:52097205-52098313	GM12878	blood:	n/a	chr19:52097710-52097719
13	TCF12	chr19:52097149-52098234	A549	lung:	n/a	chr19:52097604-52097611 chr19:52097787-52097797
14	HCFC1	chr19:52097487-52098490	K562	blood:	n/a	n/a
15	MTA3	chr19:52096806-52098235	GM12878	blood:	n/a	n/a
16	POLR2A	chr19:52097028-52098348	H1-neurons	neurons:	n/a	n/a
17	MAZ	chr19:52097043-52098242	K562	blood:	n/a	n/a
18	CTCF	chr19:52098100-52098250	HBMEC	blood vessel:	n/a	n/a
19	CTCF	chr19:52098130-52098228	GM19240	blood:	n/a	n/a
20	YY1	chr19:52097321-52098248	SK-N-SH	brain:	n/a	chr19:52098008-52098016 chr19:52097707-52097718
21	STAT1	chr19:52097229-52098267	GM12878	blood:	n/a	n/a
22	SIX5	chr19:52097441-52098228	A549	lung:	n/a	chr19:52097796-52097805 chr19:52097729-52097738 chr19:52097829-52097838
23	YY1	chr19:52097390-52098229	GM12878	blood:	n/a	chr19:52098008-52098016 chr19:52097707-52097718
24	YY1	chr19:52097529-52098265	GM12878	blood:	n/a	chr19:52098008-52098016 chr19:52097707-52097718
25	SMC3	chr19:52097571-52098257	Hela-S3	cervix:	n/a	n/a
26	ZNF384	chr19:52098154-52098290	K562	blood:	n/a	n/a
27	CTCF	chr19:52098140-52098290	A549	lung:	n/a	n/a
28	ELF1	chr19:52097425-52098225	HCT-116	colon:	n/a	chr19:52097710-52097719
29	MXI1	chr19:52096692-52098484	SK-N-SH	brain:	n/a	n/a
30	SIX5	chr19:52097302-52098209	A549	lung:	n/a	chr19:52097796-52097805 chr19:52097729-52097738 chr19:52097829-52097838
31	POLR2A	chr19:52097000-52098269	H1-neurons	neurons:	n/a	n/a
32	ZNF143	chr19:52097382-52098271	H1-hESC	embryonic stem cell:	n/a	chr19:52097822-52097840 chr19:52097729-52097738 chr19:52097722-52097740 chr19:52097831-52097840 chr19:52097789-52097807 chr19:52097796-52097805 chr19:52097829-52097838
33	REST	chr19:52096678-52098530	H1-neurons	neurons:	n/a	n/a
34	TAF1	chr19:52097667-52098284	H1-hESC	embryonic stem cell:	n/a	n/a
35	RCOR1	chr19:52097061-52098364	K562	blood:	n/a	n/a
36	TAF1	chr19:52097173-52098282	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:52097772..52099435-chr19:52099519..52102447,4	K562	blood:
2	chr19:51869850..51871538-chr19:52096656..52099033,2	K562	blood:
3	chr19:52097873..52100049-chr19:52100051..52101814,3	K562	blood:
4	chr19:51897297..51899400-chr19:52095029..52099296,3	K562	blood:
5	chr19:52073066..52077206-chr19:52096074..52099799,4	K562	blood:

Variant related genes	Relation type
ENSG00000269388	TF binding region
ENSG00000167765	TF binding region
ENSG00000267808	TF binding region
ENSG00000269403	Chromatin interaction
ENSG00000268889	Chromatin interaction
ENSG00000105497	Chromatin interaction
ENSG00000160318	Chromatin interaction
ENSG00000269388	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10412978	0.86[ASN][1000 genomes]
rs10500308	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11672358	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34390523	0.82[ASN][1000 genomes]
rs62113350	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62114988	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7255626	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066308	chr19:51680133-52103974	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv544049	chr19:51680133-52103974	Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv544051	chr19:51944903-52147459	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
5	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
6	nsv469584	chr19:52001381-52151821	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv482654	chr19:52001381-52151821	Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	25 gene(s)	inside rSNPs	diseases
8	nsv579966	chr19:52075622-52131119	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases
10	nsv9740	chr19:52096231-52107021	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52096600-52098400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr19:52096600-52098400	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr19:52096600-52098400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr19:52096600-52098400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
5	chr19:52096600-52098400	Active TSS	NHDF-Ad	bronchial
6	chr19:52096600-52098600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr19:52096600-52098600	Active TSS	A549	lung
8	chr19:52096600-52098800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:52096800-52098400	Active TSS	H9 Cell Line	embryonic stem cell
10	chr19:52096800-52098400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr19:52096800-52098400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr19:52096800-52098400	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr19:52096800-52098400	Active TSS	Fetal Intestine Large	intestine
14	chr19:52096800-52098400	Active TSS	Rectal Smooth Muscle	rectum
15	chr19:52096800-52098400	Active TSS	HSMMtube	muscle
16	chr19:52096800-52098600	Active TSS	iPS-18 Cell Line	embryonic stem cell
17	chr19:52097000-52098400	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr19:52097000-52098400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:52097000-52098400	Active TSS	HUES6 Cell Line	embryonic stem cell
20	chr19:52097000-52098400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr19:52097000-52098400	Flanking Active TSS	Primary B cells from cord blood	blood
22	chr19:52097000-52098400	Flanking Active TSS	Primary B cells from peripheral blood	blood
23	chr19:52097000-52098400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
24	chr19:52097000-52098400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr19:52097000-52098400	Active TSS	Gastric	stomach
26	chr19:52097000-52098400	Active TSS	Psoas Muscle	Psoas
27	chr19:52097000-52098600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
28	chr19:52097000-52098600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr19:52097200-52098400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:52097200-52098400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr19:52097200-52098400	Active TSS	Brain Germinal Matrix	brain
32	chr19:52097200-52098400	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr19:52097200-52098400	Active TSS	Fetal Intestine Small	intestine
34	chr19:52097200-52098400	Active TSS	Right Atrium	heart
35	chr19:52097200-52098400	Active TSS	HSMM	muscle
36	chr19:52097200-52098400	Active TSS	NHLF	lung
37	chr19:52097200-52098600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr19:52097400-52098400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr19:52097400-52098400	Active TSS	HepG2	liver
40	chr19:52097400-52098400	Active TSS	NH-A	brain
41	chr19:52097400-52098600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:52097400-52098600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr19:52097600-52098400	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr19:52097600-52098600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr19:52097800-52098400	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr19:52097800-52098400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr19:52097800-52098400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr19:52097800-52098400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr19:52097800-52098400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
50	chr19:52097800-52098400	Flanking Active TSS	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links