Variant report

Variant	rs2927479
Chromosome Location	chr19:45309886-45309887
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:45309692-45309960	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:45227043..45229115-chr19:45309849..45311993,3	MCF-7	breast:
2	chr19:45308884..45313334-chr19:45345353..45351688,18	MCF-7	breast:
3	chr19:45305840..45308889-chr19:45308989..45312130,4	MCF-7	breast:
4	chr19:45309744..45311644-chr19:45324913..45327057,2	MCF-7	breast:
5	chr19:45309587..45312322-chr19:45456957..45459370,2	MCF-7	breast:
6	chr19:45147379..45150123-chr19:45308817..45312008,3	MCF-7	breast:
7	chr19:45298818..45303552-chr19:45309335..45312129,4	MCF-7	breast:
8	chr19:45223983..45225752-chr19:45308635..45310345,2	MCF-7	breast:
9	chr19:45308022..45312966-chr19:45346579..45352259,11	MCF-7	breast:
10	chr19:45249129..45253567-chr19:45309146..45313529,6	MCF-7	breast:

No data

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

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10408993	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1075643	0.98[EUR][1000 genomes]
rs28534944	0.87[EUR][1000 genomes]
rs2927478	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2965161	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2967671	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3810140	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3810141	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7249750	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73572006	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8113171	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[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:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:45281400-45311400	Weak transcription	Right Atrium	heart
2	chr19:45284800-45311400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr19:45294200-45311600	Weak transcription	Small Intestine	intestine
4	chr19:45296200-45310600	Weak transcription	Colonic Mucosa	Colon
5	chr19:45296800-45311000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr19:45297000-45311800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr19:45298200-45310200	Weak transcription	Gastric	stomach
8	chr19:45299200-45310200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr19:45300600-45310400	Weak transcription	Stomach Mucosa	stomach
10	chr19:45300600-45311400	Weak transcription	Psoas Muscle	Psoas
11	chr19:45303800-45310600	Weak transcription	Hela-S3	cervix
12	chr19:45304000-45310400	Weak transcription	Esophagus	oesophagus
13	chr19:45304000-45310400	Weak transcription	Pancreas	Pancrea
14	chr19:45307400-45310400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr19:45307400-45311200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr19:45307600-45310200	Weak transcription	Liver	Liver
17	chr19:45307600-45310200	Weak transcription	Fetal Intestine Large	intestine
18	chr19:45307600-45310400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr19:45307600-45310600	Weak transcription	Fetal Stomach	stomach
20	chr19:45307600-45310600	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr19:45307600-45311200	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr19:45307600-45311200	Weak transcription	Spleen	Spleen
23	chr19:45307600-45311400	Weak transcription	Lung	lung
24	chr19:45307800-45311400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr19:45308000-45310200	Weak transcription	Fetal Intestine Small	intestine
26	chr19:45309400-45311200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr19:45309400-45311800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr19:45309600-45310400	Enhancers	A549	lung
29	chr19:45309600-45310400	Enhancers	HepG2	liver
30	chr19:45309600-45311200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
31	chr19:45309600-45311400	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr19:45309600-45311800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr19:45309600-45311800	Enhancers	Placenta	Placenta
34	chr19:45309600-45311800	Enhancers	HMEC	breast
35	chr19:45309600-45311800	Enhancers	NHEK	skin
36	chr19:45309800-45310000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
37	chr19:45309800-45310000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr19:45309800-45310000	Enhancers	NHLF	lung
39	chr19:45309800-45310600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
40	chr19:45309800-45310600	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
41	chr19:45309800-45311200	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr19:45309800-45311400	Enhancers	H9 Cell Line	embryonic stem cell
43	chr19:45309800-45311400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:45309800-45311400	Enhancers	Fetal Heart	heart
45	chr19:45309800-45312000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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