Variant report

Variant	rs2622744
Chromosome Location	chr3:137856784-137856785
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1137760	0.80[EUR][1000 genomes]
rs1564496	0.82[EUR][1000 genomes]
rs1600697	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2170309	0.86[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2219936	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2246945	0.86[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2251550	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2346744	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2346745	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2346747	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622694	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622695	0.86[CEU][hapmap];0.86[CHD][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2622696	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622697	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2622699	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622700	0.95[CEU][hapmap];0.90[CHB][hapmap]
rs2622714	0.84[JPT][hapmap]
rs2622732	0.81[EUR][1000 genomes]
rs2622733	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2622734	0.95[CEU][hapmap];0.89[CHB][hapmap]
rs2622735	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs2622736	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622737	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622739	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2622740	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2622742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622743	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724687	0.82[CEU][hapmap]
rs2724690	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2724691	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724692	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724710	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724711	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2724712	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2724725	0.82[EUR][1000 genomes]
rs2724726	0.91[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2724727	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[EUR][1000 genomes]
rs329380	0.80[EUR][1000 genomes]
rs3732839	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs405602	0.81[JPT][hapmap]
rs4678403	0.83[MEX][hapmap]
rs608594	0.95[CEU][hapmap];0.85[CHB][hapmap]
rs7430414	0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7613041	0.81[EUR][1000 genomes]
rs7613558	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7632402	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774803	0.95[CEU][hapmap];0.90[CHB][hapmap]
rs774807	0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap]
rs774808	0.95[CEU][hapmap];0.85[CHB][hapmap]
rs774810	0.95[CEU][hapmap];0.84[CHB][hapmap]
rs774813	0.95[CEU][hapmap];0.85[CHB][hapmap]
rs774814	0.95[CEU][hapmap];0.85[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs811811	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs9827617	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9840008	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9851548	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	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	esv2762347	chr3:137851198-137910007	Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv998106	chr3:137851198-137934610	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2622744	A4GNT	cis	Artery Tibial	GTEx
rs2622744	A4GNT	cis	Adipose Subcutaneous	GTEx
rs2622744	A4GNT	cis	Nerve Tibial	GTEx
rs2622744	A4GNT	cis	Thyroid	GTEx
rs2622744	DBR1	cis	normal skin	skin_eQTL
rs2622744	DBR1	Cis_1M	lymphoblastoid	RTeQTL
rs2622744	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx
rs2622744	A4GNT	cis	lung	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137850600-137856800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:137852200-137859400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr3:137853400-137857000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:137853400-137857600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr3:137853400-137857800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr3:137853600-137857000	Enhancers	Primary hematopoietic stem cells	blood
7	chr3:137853600-137857400	Enhancers	Primary B cells from cord blood	blood
8	chr3:137855400-137856800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:137855400-137857000	Weak transcription	Brain Substantia Nigra	brain
10	chr3:137856000-137857200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr3:137856000-137859600	Weak transcription	Stomach Mucosa	stomach
12	chr3:137856200-137857200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
13	chr3:137856400-137856800	Enhancers	Spleen	Spleen
14	chr3:137856600-137856800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:137856600-137856800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:137856600-137857000	Enhancers	Pancreas	Pancrea
17	chr3:137856600-137857200	Enhancers	Adipose Nuclei	Adipose
18	chr3:137856600-137857200	Enhancers	Gastric	stomach

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