Variant report

Variant	rs1524149
Chromosome Location	chr2:48919597-48919598
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	chr1:110595729..110598402-chr2:48919078..48921573,2	MCF-7	breast:
2	chr2:48918966..48921288-chr2:48922320..48925277,2	K562	blood:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10865234	0.94[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.80[LWK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12466526	0.89[TSI][hapmap]
rs1404052	1.00[CEU][hapmap];0.85[GIH][hapmap];0.96[EUR][1000 genomes]
rs1404053	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1404057	1.00[CHD][hapmap]
rs1464728	0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs1524150	0.87[CEU][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs1524152	0.87[EUR][1000 genomes]
rs1524158	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs1524159	0.81[EUR][1000 genomes]
rs1554613	1.00[CHD][hapmap];0.91[TSI][hapmap]
rs2204305	0.89[EUR][1000 genomes]
rs2349100	0.87[CEU][hapmap];0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2956355	1.00[CHD][hapmap]
rs4953611	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs4953617	1.00[CHD][hapmap]
rs6712571	1.00[CHD][hapmap]
rs6725150	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6725165	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6725834	1.00[CHD][hapmap]
rs6740726	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs7566301	0.81[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	nsv1010494	chr2:48767055-49027310	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1002793	chr2:48771220-49466550	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
3	nsv1004965	chr2:48796170-49443587	Bivalent Enhancer Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv535684	chr2:48796170-49443587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv498119	chr2:48808834-49422647	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv833992	chr2:48814223-48998037	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1524149	TTTY20	trans	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48863000-48919600	Weak transcription	Colon Smooth Muscle	Colon
2	chr2:48874200-48919600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:48898800-48920200	Weak transcription	Ovary	ovary
4	chr2:48908000-48920000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr2:48918000-48920800	Weak transcription	Osteobl	bone
6	chr2:48918000-48926400	Weak transcription	Adipose Nuclei	Adipose
7	chr2:48919000-48921200	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr2:48919000-48922800	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr2:48919000-48923400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr2:48919200-48921400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr2:48919200-48923400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr2:48919400-48920200	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr2:48919400-48921400	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr2:48919400-48923000	Enhancers	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links