Variant report

Variant	rs4972285
Chromosome Location	chr2:149340684-149340685
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:149337761..149341729-chr2:149349251..149353355,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000232238	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1020468	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1031290	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10454124	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10928399	0.85[EUR][1000 genomes]
rs12619201	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13004738	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16828967	0.81[AMR][1000 genomes]
rs16829006	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4972369	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4972380	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4972381	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4972383	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6743835	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6746352	0.84[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap]
rs6761549	1.00[CEU][hapmap]
rs720844	0.93[CEU][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7571333	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7590549	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7599758	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs764386	0.94[EUR][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	esv2751831	chr2:149151358-150105603	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1000101	chr2:149165813-149361220	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv868861	chr2:149198443-149434604	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv917109	chr2:149198443-149948302	ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1004663	chr2:149214090-149373061	Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	esv2762913	chr2:149249683-149345487	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4972285	NEB	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:149336800-149344200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr2:149339600-149341000	Enhancers	A549	lung
3	chr2:149339600-149341400	Enhancers	HSMMtube	muscle
4	chr2:149339800-149341000	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr2:149339800-149341000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:149339800-149341200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:149339800-149341200	Enhancers	Hela-S3	cervix
8	chr2:149339800-149341400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:149340000-149341200	Enhancers	NHEK	skin
10	chr2:149340200-149340800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr2:149340200-149341400	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr2:149340400-149340800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr2:149340400-149341000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:149340400-149341000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:149340400-149341000	Enhancers	HMEC	breast
16	chr2:149340600-149340800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr2:149340600-149340800	Enhancers	NH-A	brain
18	chr2:149340600-149341000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr2:149340600-149341000	Enhancers	HSMM	muscle
20	chr2:149340600-149341200	Enhancers	Primary B cells from peripheral blood	blood
21	chr2:149340600-149341400	Enhancers	GM12878-XiMat	blood

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