Variant report

Variant	rs2560873
Chromosome Location	chr19:52774910-52774911
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:52774064-52775003	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr19:52774608-52774927	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr19:52774588-52774946	K562	blood:	n/a	n/a
4	POLR2A	chr19:52774581-52774973	GM12891	blood:	n/a	n/a
5	POLR2A	chr19:52774105-52775017	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr19:52774681-52774989	GM12878	blood:	n/a	n/a
7	POLR2A	chr19:52774664-52774954	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr19:52774556-52774910	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr19:52774238-52775166	GM12878	blood:	n/a	n/a
10	POLR2A	chr19:52774896-52775102	HepG2	liver:	n/a	n/a
11	POLR2A	chr19:52772414-52775242	GM12878	blood:	n/a	n/a
12	POLR2A	chr19:52774889-52774956	HUVEC	blood vessel:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:52764752..52766794-chr19:52774661..52777312,2	K562	blood:
2	chr19:52772026..52776261-chr19:52781637..52786393,5	K562	blood:
3	chr19:52772363..52775107-chr19:52799601..52802037,4	MCF-7	breast:
4	chr19:52772381..52778282-chr19:52778346..52783668,9	MCF-7	breast:
5	chr19:52692994..52696358-chr19:52773094..52775949,3	MCF-7	breast:
6	chr19:52774375..52777116-chr19:52786827..52789950,3	MCF-7	breast:

No data

Variant related genes	Relation type
ZNF766	TF binding region
ENSG00000196214	Chromatin interaction
ENSG00000269102	Chromatin interaction
ENSG00000208002	Chromatin interaction
ENSG00000105568	Chromatin interaction
ENSG00000198464	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10404635	0.90[ASN][1000 genomes]
rs10425462	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10425644	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17835942	1.00[JPT][hapmap]
rs2089275	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560871	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560875	0.81[AFR][1000 genomes]
rs2560877	0.85[CHB][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2657923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657924	0.85[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657926	0.85[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2657928	0.81[AFR][1000 genomes]
rs2657930	0.85[CHB][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28718737	0.81[ASN][1000 genomes]
rs56211703	0.96[ASN][1000 genomes]
rs56369375	0.90[ASN][1000 genomes]
rs62110397	1.00[ASN][1000 genomes]
rs62110398	1.00[ASN][1000 genomes]
rs6509628	1.00[JPT][hapmap]
rs7255504	0.90[ASN][1000 genomes]
rs7255737	1.00[JPT][hapmap]
rs7256125	1.00[JPT][hapmap]
rs7256216	1.00[JPT][hapmap]
rs7256300	1.00[JPT][hapmap]
rs7256719	1.00[JPT][hapmap]
rs8107325	1.00[ASN][1000 genomes]
rs8113537	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9304726	0.85[CHB][hapmap];0.90[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	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
2	esv3366000	chr19:52491073-52842946	Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv1066015	chr19:52502213-52890308	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv544059	chr19:52502213-52890308	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52774000-52775000	Enhancers	Fetal Heart	heart
2	chr19:52774000-52775000	Enhancers	Pancreas	Pancrea
3	chr19:52774000-52775000	Enhancers	Skeletal Muscle Male	skeletal muscle
4	chr19:52774000-52775200	Enhancers	Left Ventricle	heart
5	chr19:52774000-52775600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr19:52774000-52776000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr19:52774000-52776000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr19:52774000-52776000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:52774000-52776000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr19:52774000-52776600	Weak transcription	Esophagus	oesophagus
11	chr19:52774000-52776800	Weak transcription	Psoas Muscle	Psoas
12	chr19:52774000-52780000	Weak transcription	Aorta	Aorta
13	chr19:52774000-52780200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr19:52774000-52786600	Weak transcription	Right Ventricle	heart
15	chr19:52774000-52787200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:52774200-52775000	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr19:52774200-52775000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr19:52774200-52775000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr19:52774200-52775000	Enhancers	Adipose Nuclei	Adipose
20	chr19:52774200-52775000	Enhancers	Brain Hippocampus Middle	brain
21	chr19:52774200-52775000	Genic enhancers	Fetal Muscle Leg	muscle
22	chr19:52774200-52775000	Enhancers	Gastric	stomach
23	chr19:52774200-52775000	Enhancers	HepG2	liver
24	chr19:52774200-52775600	Weak transcription	NH-A	brain
25	chr19:52774200-52776000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr19:52774200-52776000	Weak transcription	NHEK	skin
27	chr19:52774200-52777400	Weak transcription	HSMMtube	muscle
28	chr19:52774200-52786600	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr19:52774200-52797400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr19:52774200-52799600	Weak transcription	Hela-S3	cervix
31	chr19:52774400-52775000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr19:52774400-52775000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr19:52774400-52775000	Enhancers	Brain Germinal Matrix	brain
34	chr19:52774400-52775000	Genic enhancers	Duodenum Mucosa	Duodenum
35	chr19:52774400-52775200	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr19:52774400-52775400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr19:52774400-52775600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr19:52774400-52775600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
39	chr19:52774400-52775600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:52774400-52775600	Enhancers	Duodenum Smooth Muscle	Duodenum
41	chr19:52774400-52775800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr19:52774400-52775800	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr19:52774400-52776000	Strong transcription	HSMM	muscle
44	chr19:52774400-52777000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
45	chr19:52774400-52777200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr19:52774400-52777200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
47	chr19:52774400-52777600	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr19:52774400-52777800	ZNF genes & repeats	A549	lung
49	chr19:52774400-52778400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
50	chr19:52774400-52778400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood

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