Variant report

Variant	rs485152
Chromosome Location	chr19:56148389-56148390
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:56146082-56149393	GM12892	blood:	n/a	n/a
2	POLR2A	chr19:56146092-56148563	GM12878	blood:	n/a	n/a
3	POLR2A	chr19:56146070-56148494	GM12891	blood:	n/a	n/a
4	POLR2A	chr19:56146049-56148415	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:56148125-56148448	HepG2	liver:	n/a	n/a
6	POLR2A	chr19:56147905-56148481	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:56147925-56148480	K562	blood:	n/a	n/a
8	POLR2A	chr19:56146108-56148514	GM12891	blood:	n/a	n/a
9	POLR2A	chr19:56146066-56155822	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr19:56145990-56148670	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr19:56146089-56148481	GM18505	blood:	n/a	n/a
12	POLR2A	chr19:56146054-56148535	GM12878	blood:	n/a	n/a
13	POLR2A	chr19:56146111-56148468	IMR90	lung:	n/a	n/a
14	POLR2A	chr19:56145947-56149686	SK-N-MC	brain:	n/a	n/a
15	POLR2A	chr19:56146054-56148734	GM12891	blood:	n/a	n/a
16	POLR2A	chr19:56146111-56148523	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr19:56146995-56149583	K562	blood:	n/a	n/a
18	POLR2A	chr19:56148175-56148721	K562	blood:	n/a	n/a
19	POLR2A	chr19:56145941-56148656	GM12892	blood:	n/a	n/a
20	POLR2A	chr19:56145999-56149668	GM12878	blood:	n/a	n/a
21	POLR2A	chr19:56147876-56148438	GM12878	blood:	n/a	n/a
22	POLR2A	chr19:56147675-56148588	MCF10A-Er-Src	breast:	n/a	n/a
23	POLR2A	chr19:56148119-56148495	GM12892	blood:	n/a	n/a
24	POLR2A	chr19:56146047-56148543	GM12892	blood:	n/a	n/a
25	POLR2A	chr19:56146014-56148713	PANC-1	pancreas:	n/a	n/a
26	POLR2A	chr19:56146039-56148828	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:55895074..55897174-chr19:56145786..56148520,2	MCF-7	breast:
2	chr19:56109995..56114029-chr19:56145200..56149074,4	MCF-7	breast:
3	chr19:56135345..56138507-chr19:56147845..56151809,4	K562	blood:
4	chr19:55917719..55921194-chr19:56143842..56149725,7	K562	blood:
5	chr19:56134501..56137412-chr19:56145689..56149345,6	K562	blood:

No data

Variant related genes	Relation type
ZNF580	TF binding region
ZNF581	TF binding region
CCDC106	TF binding region
ENSG00000108107	Chromatin interaction
ENSG00000171443	Chromatin interaction
ENSG00000179922	Chromatin interaction
ENSG00000179943	Chromatin interaction
ENSG00000108106	Chromatin interaction
ENSG00000233493	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1808393	0.95[ASN][1000 genomes]
rs2864434	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs310436	0.91[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs504850	0.95[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs519856	0.91[ASN][1000 genomes]
rs579496	0.93[ASN][1000 genomes]
rs596075	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs643368	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs664684	0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7247677	0.91[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs7249837	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7252055	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8791	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs889092	1.00[CHB][hapmap];0.91[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:56146400-56148400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr19:56146600-56148400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
3	chr19:56146800-56148400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr19:56146800-56148400	Flanking Active TSS	Duodenum Mucosa	Duodenum
5	chr19:56146800-56148400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr19:56146800-56148400	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr19:56147000-56148400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:56147000-56148400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
9	chr19:56147200-56148400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr19:56147200-56148400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr19:56147200-56148400	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr19:56147200-56148400	Flanking Active TSS	HepG2	liver
13	chr19:56147200-56148600	Flanking Active TSS	GM12878-XiMat	blood
14	chr19:56147400-56148400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr19:56147400-56148400	Enhancers	Primary monocytes fromperipheralblood	blood
16	chr19:56147400-56148400	Enhancers	Aorta	Aorta
17	chr19:56147400-56148600	Enhancers	Primary neutrophils fromperipheralblood	blood
18	chr19:56147400-56148600	Enhancers	Placenta	Placenta
19	chr19:56147400-56149200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:56147400-56149200	Genic enhancers	Fetal Muscle Leg	muscle
21	chr19:56147400-56149800	Enhancers	Gastric	stomach
22	chr19:56147600-56148400	Enhancers	Esophagus	oesophagus
23	chr19:56147600-56148400	Enhancers	Fetal Lung	lung
24	chr19:56147600-56148400	Enhancers	Fetal Thymus	thymus
25	chr19:56147600-56148400	Enhancers	Right Atrium	heart
26	chr19:56147600-56148600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr19:56147600-56148600	Enhancers	Left Ventricle	heart
28	chr19:56147600-56148600	Enhancers	Right Ventricle	heart
29	chr19:56147600-56149000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr19:56147600-56149000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
31	chr19:56147600-56149000	Enhancers	Fetal Muscle Trunk	muscle
32	chr19:56147600-56149200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr19:56147600-56149200	Enhancers	Primary B cells from cord blood	blood
34	chr19:56147600-56149200	Enhancers	Primary B cells from peripheral blood	blood
35	chr19:56147600-56149200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:56147600-56149200	Enhancers	Brain Germinal Matrix	brain
37	chr19:56147600-56149400	Enhancers	Ovary	ovary
38	chr19:56147600-56149400	Enhancers	Spleen	Spleen
39	chr19:56147600-56149600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:56147600-56150400	Weak transcription	Fetal Brain Female	brain
41	chr19:56147800-56148400	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr19:56147800-56148400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr19:56147800-56148400	Enhancers	Brain Anterior Caudate	brain
44	chr19:56147800-56148400	Enhancers	Colonic Mucosa	Colon
45	chr19:56147800-56148400	Genic enhancers	Lung	lung
46	chr19:56147800-56148400	Enhancers	Rectal Mucosa Donor 31	rectum
47	chr19:56147800-56148400	Enhancers	Rectal Smooth Muscle	rectum
48	chr19:56147800-56148400	Enhancers	K562	blood
49	chr19:56147800-56148400	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr19:56147800-56148400	Active TSS	NHLF	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links