Variant report

Variant	rs13025888
Chromosome Location	chr2:152097199-152097200
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	chr2:152096466..152099037-chr2:152145207..152147647,2	K562	blood:
2	chr2:152096040..152098295-chr2:152099658..152101934,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123609	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1048135	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11678123	0.81[ASN][1000 genomes]
rs11680338	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11683487	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11690634	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs11691055	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11691217	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11730	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12467046	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12471191	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12476687	0.80[ASN][1000 genomes]
rs12624156	0.91[ASN][1000 genomes]
rs12693004	0.91[ASN][1000 genomes]
rs12987765	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12994801	0.83[AFR][1000 genomes]
rs12996459	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13001328	0.81[ASN][1000 genomes]
rs13004590	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13020962	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13027425	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13029661	0.83[AFR][1000 genomes]
rs1518687	0.83[AFR][1000 genomes]
rs17797018	0.83[AFR][1000 genomes]
rs17798290	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2113508	0.88[ASN][1000 genomes]
rs2218880	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2271811	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2278090	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2880488	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs289904	0.88[EUR][1000 genomes]
rs289905	0.88[EUR][1000 genomes]
rs289906	0.90[EUR][1000 genomes]
rs289907	0.88[EUR][1000 genomes]
rs289921	0.87[EUR][1000 genomes]
rs289923	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs289924	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34028108	0.89[ASN][1000 genomes]
rs34452578	0.84[ASN][1000 genomes]
rs34538548	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs35659175	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35723696	0.81[ASN][1000 genomes]
rs35863408	0.81[ASN][1000 genomes]
rs3771882	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3854012	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3856557	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4664280	0.83[AFR][1000 genomes]
rs4664336	0.81[ASN][1000 genomes]
rs4664347	0.81[ASN][1000 genomes]
rs4664349	0.81[ASN][1000 genomes]
rs4665114	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4665137	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4665150	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4665168	0.90[ASN][1000 genomes]
rs55775354	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56335263	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs56376752	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57201382	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs66521733	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66588921	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67303849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739517	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67725431	0.91[ASN][1000 genomes]
rs67788715	0.83[AFR][1000 genomes]
rs7558169	0.81[ASN][1000 genomes]
rs7559296	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7574228	0.81[ASN][1000 genomes]
rs7587037	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs958525	0.83[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523849	chr2:151718133-152143524	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	esv3693426	chr2:151725792-152295862	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv834417	chr2:151980473-152154950	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv1014936	chr2:152019809-152118479	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1012891	chr2:152019809-152306897	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13025888	TNFAIP6	cis	Whole Blood	GTEx
rs13025888	NMI	Cis_1M	lymphoblastoid	RTeQTL
rs13025888	RBM43	cis	Whole Blood	GTEx
rs13025888	TNFAIP6	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152092600-152103000	Weak transcription	Ovary	ovary
2	chr2:152093000-152105200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:152094400-152097400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr2:152094400-152105000	Weak transcription	Adipose Nuclei	Adipose
5	chr2:152094400-152105000	Weak transcription	Liver	Liver
6	chr2:152094400-152105200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:152094400-152117000	Weak transcription	A549	lung
8	chr2:152095000-152097400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:152095200-152105200	Weak transcription	Osteobl	bone
10	chr2:152095400-152105200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:152095400-152107200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:152095600-152105200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:152096000-152104400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:152096000-152105200	Weak transcription	NHDF-Ad	bronchial
15	chr2:152096800-152098200	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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