Variant report

Variant	rs2724687
Chromosome Location	chr3:137840903-137840904
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:137833036..137835902-chr3:137839333..137840935,2	K562	blood:
2	chr3:137840738..137842878-chr3:137891871..137893795,3	K562	blood:

Variant related genes	Relation type
ENSG00000138231	Chromatin interaction
ENSG00000158163	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs1107422	0.88[ASN][1000 genomes]
rs11719358	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs13100360	0.91[ASN][1000 genomes]
rs1351446	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1545816	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1564496	0.97[ASN][1000 genomes]
rs17838821	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs179282	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2170309	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2219936	0.82[CEU][hapmap]
rs2246945	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2622694	0.82[CEU][hapmap]
rs2622695	0.95[CEU][hapmap]
rs2622697	0.97[ASN][1000 genomes]
rs2622698	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622704	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2622705	0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2622706	0.83[ASN][1000 genomes]
rs2622707	0.83[ASN][1000 genomes]
rs2622709	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2622710	0.86[ASN][1000 genomes]
rs2622711	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2622714	0.87[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2622715	0.89[ASN][1000 genomes]
rs2622716	0.89[ASN][1000 genomes]
rs2622717	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2622718	0.89[ASN][1000 genomes]
rs2622719	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2622720	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2622727	0.91[ASN][1000 genomes]
rs2622728	0.91[ASN][1000 genomes]
rs2622729	0.91[ASN][1000 genomes]
rs2622730	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2622745	0.86[ASN][1000 genomes]
rs2622746	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2724679	0.90[ASN][1000 genomes]
rs2724691	0.82[CEU][hapmap]
rs2724692	0.82[CEU][hapmap]
rs2724693	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2724694	0.85[ASN][1000 genomes]
rs2724695	0.82[ASN][1000 genomes]
rs2724697	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2724698	0.83[ASN][1000 genomes]
rs2724699	0.83[ASN][1000 genomes]
rs2724700	0.83[ASN][1000 genomes]
rs2724701	0.83[ASN][1000 genomes]
rs2724702	0.83[ASN][1000 genomes]
rs2724704	0.83[ASN][1000 genomes]
rs2724705	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2724706	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2724707	1.00[JPT][hapmap]
rs2724708	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2724716	0.91[ASN][1000 genomes]
rs2724717	0.88[ASN][1000 genomes]
rs2724729	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs28480035	0.86[ASN][1000 genomes]
rs329381	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs329382	0.82[ASN][1000 genomes]
rs329383	0.89[ASN][1000 genomes]
rs329384	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs329385	0.91[ASN][1000 genomes]
rs329388	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs329389	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs329390	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs329391	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs365504	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs367439	0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs374045	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs382629	0.88[CHB][hapmap];0.95[JPT][hapmap]
rs384828	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs390729	0.88[ASN][1000 genomes]
rs405265	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs405602	0.88[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs407009	0.83[ASN][1000 genomes]
rs419075	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs442800	0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs446644	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs452195	0.83[ASN][1000 genomes]
rs453023	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs4678403	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs618553	0.86[ASN][1000 genomes]
rs6809258	0.88[ASN][1000 genomes]
rs7613955	0.88[ASN][1000 genomes]
rs7629243	0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7639197	0.89[ASN][1000 genomes]
rs899983	0.88[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9812778	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9834462	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9842648	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9842918	0.95[ASN][1000 genomes]
rs9857908	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9860229	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9860630	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9874211	0.90[ASN][1000 genomes]
rs996432	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][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	nsv530056	chr3:137312356-138161861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	esv2757890	chr3:137611789-137933835	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv2759180	chr3:137611789-137933835	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2751978	chr3:137715302-137890750	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1007857	chr3:137767454-137843106	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2724687	A4GNT	cis	Nerve Tibial	GTEx
rs2724687	A4GNT	cis	Thyroid	GTEx
rs2724687	DBR1	Cis_1M	lymphoblastoid	RTeQTL
rs2724687	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137834800-137843000	Weak transcription	Placenta	Placenta
2	chr3:137834800-137843600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:137835000-137843600	Weak transcription	Right Ventricle	heart
4	chr3:137835200-137843200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:137835200-137843600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr3:137835200-137843600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:137835200-137843600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr3:137835400-137843400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:137835400-137844200	Weak transcription	A549	lung
10	chr3:137835800-137843600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:137838000-137843400	Weak transcription	Osteobl	bone
12	chr3:137838000-137843600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr3:137838000-137844600	Weak transcription	Adipose Nuclei	Adipose
14	chr3:137838200-137843600	Weak transcription	Fetal Heart	heart
15	chr3:137838400-137843600	Weak transcription	Fetal Muscle Trunk	muscle
16	chr3:137838400-137843600	Weak transcription	Hela-S3	cervix
17	chr3:137839600-137843000	Weak transcription	Primary neutrophils fromperipheralblood	blood

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