Variant report

Variant	rs4953611
Chromosome Location	chr2:48920263-48920264
allele	C/T
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: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10204790	0.82[ASW][hapmap];0.89[YRI][hapmap]
rs10865234	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs11890355	0.82[YRI][hapmap]
rs12466526	0.81[ASW][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap]
rs12468825	1.00[ASW][hapmap];0.81[AMR][1000 genomes]
rs12469348	0.81[ASW][hapmap]
rs12472054	0.80[AFR][1000 genomes]
rs13396590	0.94[YRI][hapmap]
rs1404052	0.91[ASW][hapmap];1.00[CEU][hapmap];0.85[GIH][hapmap];0.98[MKK][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1404053	1.00[CEU][hapmap];0.94[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1404057	1.00[CHD][hapmap]
rs1464728	1.00[ASW][hapmap];0.87[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1524149	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs1524150	0.87[CEU][hapmap];0.89[EUR][1000 genomes]
rs1524152	0.82[EUR][1000 genomes]
rs1524158	0.82[CEU][hapmap];0.93[YRI][hapmap]
rs1554613	0.92[ASW][hapmap];1.00[CHD][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap]
rs2177485	0.83[AFR][1000 genomes]
rs2204305	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2349100	0.87[CEU][hapmap];0.96[EUR][1000 genomes]
rs2956355	1.00[CHD][hapmap]
rs4953617	1.00[CHD][hapmap]
rs6712571	1.00[CHD][hapmap]
rs6725150	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs6725165	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6725834	1.00[CHD][hapmap]
rs6740726	1.00[CEU][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6747134	0.94[YRI][hapmap]

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
rs4953611	TTTY20	trans	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48918000-48920800	Weak transcription	Osteobl	bone
2	chr2:48918000-48926400	Weak transcription	Adipose Nuclei	Adipose
3	chr2:48919000-48921200	Enhancers	HUES48 Cell Line	embryonic stem cell
4	chr2:48919000-48922800	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr2:48919000-48923400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:48919200-48921400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr2:48919200-48923400	Enhancers	HUES64 Cell Line	embryonic stem cell
8	chr2:48919400-48921400	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr2:48919400-48923000	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr2:48919600-48920400	Enhancers	Colon Smooth Muscle	Colon
11	chr2:48919600-48920600	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr2:48919600-48920600	Enhancers	NH-A	brain
13	chr2:48919600-48922400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:48919600-48922600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr2:48919800-48920800	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:48919800-48926600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:48920000-48921400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:48920000-48921800	Enhancers	Stomach Smooth Muscle	stomach
19	chr2:48920200-48920400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:48920200-48920800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr2:48920200-48921000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr2:48920200-48921600	Enhancers	Ovary	ovary
23	chr2:48920200-48926600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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