Variant report

Variant	rs13105287
Chromosome Location	chr4:106900159-106900160
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:106899986..106902171-chr4:106913002..106915324,2	K562	blood:
2	chr4:106893048..106895457-chr4:106896581..106900704,4	K562	blood:
3	chr14:24562244..24564068-chr4:106897955..106900240,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100889	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs11097908	0.84[EUR][1000 genomes]
rs13132677	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138279	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13147201	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13147392	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13150451	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13150647	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13151138	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1573480	0.81[EUR][1000 genomes]
rs17036476	0.84[EUR][1000 genomes]
rs17258724	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1893717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1893719	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1893720	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2156508	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2156509	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2156510	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2187357	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28788806	0.81[AMR][1000 genomes]
rs28838601	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28863615	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34000647	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34160816	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34371905	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34725554	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35270545	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35304718	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35363492	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35436827	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4295264	0.85[AMR][1000 genomes]
rs4320139	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4507364	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4527479	1.00[YRI][hapmap]
rs4698954	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6419173	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533229	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6533230	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6533231	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6533232	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66720770	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6826176	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6840126	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs71599076	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71599077	0.86[AMR][1000 genomes]
rs71599078	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7659168	0.83[AMR][1000 genomes]
rs7669422	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7670195	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7670232	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7671109	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7676845	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7677290	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7683740	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7683941	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7691229	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7691244	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7691395	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7691403	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7691953	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs869928	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014993	chr4:106796019-106980727	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522792	chr4:106895964-106982793	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv290813	chr4:106897031-106900926	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13105287	AGXT2L1	cis	parietal	SCAN
rs13105287	TBCK	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106885400-106909800	Weak transcription	Aorta	Aorta
2	chr4:106897800-106900600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:106897800-106901400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:106899600-106900600	Enhancers	NHEK	skin
5	chr4:106900000-106900400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:106900000-106900400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr4:106900000-106900400	Enhancers	Adipose Nuclei	Adipose
8	chr4:106900000-106900600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr4:106900000-106900800	Enhancers	HUVEC	blood vessel
10	chr4:106900000-106901000	Enhancers	HSMMtube	muscle
11	chr4:106900000-106901000	Enhancers	Osteobl	bone

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