Variant report

Variant	rs28742260
Chromosome Location	chr19:45309720-45309721
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:45309530-45309765	HCT-116	colon:	n/a	n/a
2	POLR2A	chr19:45309692-45309960	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr19:45309688-45309747	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:45308884..45313334-chr19:45345353..45351688,18	MCF-7	breast:
2	chr19:45305840..45308889-chr19:45308989..45312130,4	MCF-7	breast:
3	chr19:45309587..45312322-chr19:45456957..45459370,2	MCF-7	breast:
4	chr19:45147379..45150123-chr19:45308817..45312008,3	MCF-7	breast:
5	chr19:45298818..45303552-chr19:45309335..45312129,4	MCF-7	breast:
6	chr19:45223983..45225752-chr19:45308635..45310345,2	MCF-7	breast:
7	chr19:45308022..45312966-chr19:45346579..45352259,11	MCF-7	breast:
8	chr19:45249129..45253567-chr19:45309146..45313529,6	MCF-7	breast:

No data

Variant related genes	Relation type
BCAM	TF binding region
ENSG00000069399	Chromatin interaction
ENSG00000267114	Chromatin interaction
ENSG00000073008	Chromatin interaction
ENSG00000130202	Chromatin interaction
ENSG00000104853	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs12609306	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28399603	0.95[ASN][1000 genomes]
rs28399608	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3745159	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs748913	0.96[ASN][1000 genomes]
rs8101274	1.00[EUR][1000 genomes]
rs922387	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv912117	chr19:45298069-45322744	Weak transcription Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
2	nsv912118	chr19:45300056-45326664	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv912119	chr19:45304307-45317089	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv912120	chr19:45304307-45317469	Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	nsv912121	chr19:45304307-45319297	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv912122	chr19:45304307-45324516	Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45281400-45311400	Weak transcription	Right Atrium	heart
2	chr19:45284600-45309800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:45284800-45311400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr19:45294200-45311600	Weak transcription	Small Intestine	intestine
5	chr19:45296200-45310600	Weak transcription	Colonic Mucosa	Colon
6	chr19:45296800-45311000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr19:45297000-45311800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr19:45298200-45310200	Weak transcription	Gastric	stomach
9	chr19:45299200-45310200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr19:45300600-45310400	Weak transcription	Stomach Mucosa	stomach
11	chr19:45300600-45311400	Weak transcription	Psoas Muscle	Psoas
12	chr19:45303800-45310600	Weak transcription	Hela-S3	cervix
13	chr19:45304000-45309800	Weak transcription	Fetal Heart	heart
14	chr19:45304000-45310400	Weak transcription	Esophagus	oesophagus
15	chr19:45304000-45310400	Weak transcription	Pancreas	Pancrea
16	chr19:45307400-45310400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr19:45307400-45311200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr19:45307600-45310200	Weak transcription	Liver	Liver
19	chr19:45307600-45310200	Weak transcription	Fetal Intestine Large	intestine
20	chr19:45307600-45310400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr19:45307600-45310600	Weak transcription	Fetal Stomach	stomach
22	chr19:45307600-45310600	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr19:45307600-45311200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr19:45307600-45311200	Weak transcription	Spleen	Spleen
25	chr19:45307600-45311400	Weak transcription	Lung	lung
26	chr19:45307800-45311400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr19:45308000-45310200	Weak transcription	Fetal Intestine Small	intestine
28	chr19:45309400-45311200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:45309400-45311800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:45309600-45309800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
31	chr19:45309600-45310400	Enhancers	A549	lung
32	chr19:45309600-45310400	Enhancers	HepG2	liver
33	chr19:45309600-45311200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
34	chr19:45309600-45311400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr19:45309600-45311800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr19:45309600-45311800	Enhancers	Placenta	Placenta
37	chr19:45309600-45311800	Enhancers	HMEC	breast
38	chr19:45309600-45311800	Enhancers	NHEK	skin

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