Variant report

Variant	rs11125589
Chromosome Location	chr2:55941440-55941441
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	chr2:55919171..55920952-chr2:55938967..55941895,2	MCF-7	breast:
2	chr2:55939884..55941673-chr2:55943999..55946003,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1045910	0.87[CHD][hapmap]
rs1084523	0.92[ASN][1000 genomes]
rs11125586	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11125587	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11125588	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12474717	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12617829	0.83[AMR][1000 genomes]
rs12623877	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12713302	0.83[ASN][1000 genomes]
rs13430657	0.80[ASN][1000 genomes]
rs2586949	0.81[CHD][hapmap]
rs2627757	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2627761	0.82[ASN][1000 genomes]
rs2627763	0.87[CHD][hapmap]
rs3748945	0.81[CHD][hapmap]
rs3816489	0.81[CHD][hapmap]
rs4671248	0.81[CHD][hapmap]
rs55684837	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56396684	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57665392	1.00[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs58727204	1.00[ASN][1000 genomes]
rs66606456	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6705570	0.92[ASN][1000 genomes]
rs6743072	0.89[ASN][1000 genomes]
rs706549	0.89[CHD][hapmap]
rs706550	0.90[CEU][hapmap];0.82[CHB][hapmap]
rs706551	0.87[CHD][hapmap]
rs72812173	1.00[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs782574	0.85[CHD][hapmap]
rs782583	0.87[CHD][hapmap]
rs782591	0.84[CHD][hapmap]
rs782593	0.84[CHD][hapmap]
rs782608	0.87[ASN][1000 genomes]
rs782609	0.92[ASN][1000 genomes]
rs782610	0.88[ASN][1000 genomes]
rs782611	0.90[ASN][1000 genomes]
rs782620	0.91[CHD][hapmap]
rs782621	0.86[CHB][hapmap]
rs782628	0.90[CEU][hapmap];0.86[CHB][hapmap];0.83[AMR][1000 genomes]
rs782636	0.87[CHD][hapmap]
rs9636439	0.81[CHD][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	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
6	esv2760573	chr2:55903016-55941440	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11125589	CCDC85A	cis	parietal	SCAN
rs11125589	CCDC88A	cis	cerebellum	SCAN
rs11125589	PNPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55939400-55943600	Enhancers	Fetal Intestine Small	intestine
2	chr2:55939400-55943800	Enhancers	Fetal Intestine Large	intestine
3	chr2:55939600-55943200	Enhancers	Rectal Mucosa Donor 31	rectum
4	chr2:55940000-55941800	Weak transcription	HepG2	liver
5	chr2:55940000-55945600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:55940200-55945600	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr2:55940200-55945600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr2:55940200-55945600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr2:55940200-55945600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr2:55940200-55945800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:55940800-55941600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr2:55940800-55942200	Weak transcription	Duodenum Mucosa	Duodenum
13	chr2:55940800-55950600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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