Variant report

Variant	rs12033453
Chromosome Location	chr1:225846530-225846531
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225843047..225846834-chr1:225854050..225856765,3	MCF-7	breast:
2	chr1:225845487..225847211-chr1:225869502..225871326,2	MCF-7	breast:
3	chr1:225844790..225847671-chr1:226111498..226113451,2	MCF-7	breast:
4	chr1:225840113..225842688-chr1:225846092..225848913,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ENAH-3	chr1:225846074-225846574	NONHSAT009843

Variant related genes	Relation type
ENSG00000143811	Chromatin interaction
ENSG00000154380	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10429871	0.96[ASN][1000 genomes]
rs12027872	0.92[ASN][1000 genomes]
rs12038461	0.90[ASN][1000 genomes]
rs12038893	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12039453	0.93[ASN][1000 genomes]
rs12043837	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs16845153	0.87[ASN][1000 genomes]
rs1870834	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56793390	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs74147627	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832725	chr1:225726998-225910121	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225842000-225865000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:225842200-225846600	Enhancers	Fetal Muscle Leg	muscle
3	chr1:225842200-225847200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr1:225843000-225852400	Weak transcription	Psoas Muscle	Psoas
5	chr1:225843600-225848000	Weak transcription	Brain Substantia Nigra	brain
6	chr1:225843800-225848000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:225844000-225854000	Weak transcription	Fetal Lung	lung
8	chr1:225844200-225846600	Enhancers	NHLF	lung
9	chr1:225845400-225848000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr1:225845600-225847800	Weak transcription	Adipose Nuclei	Adipose
11	chr1:225845600-225848200	Weak transcription	Fetal Stomach	stomach
12	chr1:225845600-225850200	Weak transcription	Lung	lung
13	chr1:225845600-225852200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:225845600-225858400	Weak transcription	Right Atrium	heart
15	chr1:225845800-225846800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:225845800-225848200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:225845800-225848400	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:225845800-225849400	Weak transcription	Fetal Heart	heart
19	chr1:225846000-225846600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr1:225846000-225846600	Enhancers	Fetal Muscle Trunk	muscle
21	chr1:225846000-225848200	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:225846000-225848200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr1:225846000-225858000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:225846200-225846600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:225846200-225846600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr1:225846200-225846600	Enhancers	NHDF-Ad	bronchial
27	chr1:225846200-225846600	Enhancers	Osteobl	bone
28	chr1:225846200-225847800	Weak transcription	HUVEC	blood vessel
29	chr1:225846200-225848200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr1:225846200-225848200	Weak transcription	A549	lung
31	chr1:225846200-225849400	Weak transcription	NH-A	brain
32	chr1:225846400-225846600	Enhancers	Fetal Thymus	thymus
33	chr1:225846400-225850200	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links