Variant report

Variant	rs13430657
Chromosome Location	chr2:55948428-55948429
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	chr2:55941986..55943546-chr2:55946701..55948891,2	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1045910	0.92[EUR][1000 genomes]
rs1084523	0.83[ASN][1000 genomes]
rs11125586	0.83[ASN][1000 genomes]
rs11125587	0.83[ASN][1000 genomes]
rs11125588	0.81[ASN][1000 genomes]
rs11125589	0.80[ASN][1000 genomes]
rs12474717	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12619756	0.88[EUR][1000 genomes]
rs12713301	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13427693	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1373228	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1975485	0.88[EUR][1000 genomes]
rs1975486	0.85[EUR][1000 genomes]
rs2586946	0.80[EUR][1000 genomes]
rs2586948	0.80[EUR][1000 genomes]
rs2586949	0.80[EUR][1000 genomes]
rs2586951	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2586955	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2586958	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2586959	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2586960	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2586961	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2586965	0.93[EUR][1000 genomes]
rs2627757	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2627758	0.95[EUR][1000 genomes]
rs2627763	0.90[EUR][1000 genomes]
rs2627768	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2627774	1.00[EUR][1000 genomes]
rs2627778	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2627781	0.82[EUR][1000 genomes]
rs56396684	0.84[ASN][1000 genomes]
rs57665392	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs58727204	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs66606456	0.83[ASN][1000 genomes]
rs6705570	0.83[ASN][1000 genomes]
rs6743072	0.80[ASN][1000 genomes]
rs706549	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs706551	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72812173	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7559307	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7605486	0.90[EUR][1000 genomes]
rs782569	0.97[EUR][1000 genomes]
rs782570	1.00[EUR][1000 genomes]
rs782571	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs782574	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs782575	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs782576	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs782577	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs782580	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs782582	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs782583	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs782589	0.95[EUR][1000 genomes]
rs782591	0.95[EUR][1000 genomes]
rs782593	0.90[EUR][1000 genomes]
rs782598	0.80[EUR][1000 genomes]
rs782603	0.95[EUR][1000 genomes]
rs782604	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs782605	0.82[EUR][1000 genomes]
rs782609	0.83[ASN][1000 genomes]
rs782611	0.81[ASN][1000 genomes]
rs782612	0.93[EUR][1000 genomes]
rs782615	1.00[EUR][1000 genomes]
rs782617	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs782618	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs782620	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs782621	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs782623	0.97[EUR][1000 genomes]
rs782624	1.00[EUR][1000 genomes]
rs782625	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs782626	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs782627	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs782631	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs782635	0.95[EUR][1000 genomes]
rs782636	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs782638	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs782643	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs782647	0.90[EUR][1000 genomes]
rs782648	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs782651	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531374	chr2:55653723-56299784	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	esv2757798	chr2:55747239-55981074	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2759050	chr2:55747239-55981074	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv1008452	chr2:55809191-55987274	Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	esv2762645	chr2:55892248-55963418	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13430657	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55940800-55950600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr2:55943200-55948800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:55946000-55948600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr2:55946000-55948800	Weak transcription	A549	lung
5	chr2:55946400-55948800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:55946800-55954400	Weak transcription	Fetal Intestine Small	intestine
7	chr2:55947600-55949200	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr2:55947600-55949400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:55947800-55948800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:55948200-55949000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:55948200-55949000	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr2:55948200-55949000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:55948200-55949800	Enhancers	Muscle Satellite Cultured Cells	--
14	chr2:55948400-55948800	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:55948400-55949600	Enhancers	HMEC	breast

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