Variant report

Variant	rs2246945
Chromosome Location	chr3:137843476-137843477
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 131 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:127)

rs_ID	r²[population]
rs1107422	0.85[ASN][1000 genomes]
rs11719358	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs13100360	0.88[ASN][1000 genomes]
rs1351446	0.97[ASN][1000 genomes]
rs1545816	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1564496	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1600697	0.81[EUR][1000 genomes]
rs17838821	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs179282	0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap]
rs2170309	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2219936	0.86[CEU][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2346747	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2622694	0.86[CEU][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2622695	1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2622696	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2622697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622698	0.97[ASN][1000 genomes]
rs2622699	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2622700	0.81[CEU][hapmap]
rs2622704	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2622705	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2622706	0.80[ASN][1000 genomes]
rs2622707	0.80[ASN][1000 genomes]
rs2622709	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2622710	0.83[ASN][1000 genomes]
rs2622711	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs2622714	1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2622715	0.86[ASN][1000 genomes]
rs2622716	0.86[ASN][1000 genomes]
rs2622717	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2622718	0.86[ASN][1000 genomes]
rs2622719	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2622720	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2622727	0.88[ASN][1000 genomes]
rs2622728	0.88[ASN][1000 genomes]
rs2622729	0.88[ASN][1000 genomes]
rs2622730	0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2622733	0.81[CEU][hapmap]
rs2622734	0.81[CEU][hapmap]
rs2622735	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs2622736	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs2622737	0.81[CEU][hapmap]
rs2622742	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2622743	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2622744	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2622745	0.89[ASN][1000 genomes]
rs2622746	0.95[ASN][1000 genomes]
rs2724679	0.87[ASN][1000 genomes]
rs2724687	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2724690	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2724691	0.86[CEU][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2724692	0.86[CEU][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2724693	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2724694	0.88[ASN][1000 genomes]
rs2724697	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2724698	0.80[ASN][1000 genomes]
rs2724699	0.80[ASN][1000 genomes]
rs2724700	0.80[ASN][1000 genomes]
rs2724701	0.80[ASN][1000 genomes]
rs2724702	0.80[ASN][1000 genomes]
rs2724703	0.83[ASN][1000 genomes]
rs2724704	0.80[ASN][1000 genomes]
rs2724705	0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2724706	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2724707	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2724708	0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2724711	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2724712	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs2724716	0.88[ASN][1000 genomes]
rs2724717	0.90[ASN][1000 genomes]
rs2724726	0.83[MEX][hapmap]
rs2724727	0.81[CEU][hapmap]
rs2724729	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28480035	0.84[ASN][1000 genomes]
rs329381	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs329382	0.85[ASN][1000 genomes]
rs329383	0.86[ASN][1000 genomes]
rs329384	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs329385	0.88[ASN][1000 genomes]
rs329388	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs329389	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs329390	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs329391	0.93[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs365504	0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs367439	0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs3732839	0.81[CEU][hapmap]
rs374045	0.87[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs382629	0.87[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs384828	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs389697	0.80[ASN][1000 genomes]
rs390729	0.90[ASN][1000 genomes]
rs405265	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs405602	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs407009	0.80[ASN][1000 genomes]
rs419075	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs425938	0.83[ASN][1000 genomes]
rs442800	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs445025	0.83[ASN][1000 genomes]
rs446644	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs452195	0.80[ASN][1000 genomes]
rs453023	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4678403	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608594	0.81[CEU][hapmap]
rs618553	0.83[ASN][1000 genomes]
rs6809258	0.86[ASN][1000 genomes]
rs7613558	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7613955	0.90[ASN][1000 genomes]
rs7629243	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs7632402	0.81[EUR][1000 genomes]
rs7639197	0.86[ASN][1000 genomes]
rs774803	0.81[CEU][hapmap]
rs774807	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs774808	0.81[CEU][hapmap]
rs774810	0.81[CEU][hapmap]
rs774813	0.81[CEU][hapmap]
rs774814	0.81[CEU][hapmap]
rs811811	0.81[CEU][hapmap]
rs899983	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9812778	0.93[ASN][1000 genomes]
rs9834462	0.95[ASN][1000 genomes]
rs9842648	0.95[ASN][1000 genomes]
rs9842918	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9857908	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9860229	0.95[ASN][1000 genomes]
rs9860630	0.91[ASN][1000 genomes]
rs9874211	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs996432	0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2246945	DBR1	Cis_1M	lymphoblastoid	RTeQTL
rs2246945	A4GNT	cis	Artery Tibial	GTEx
rs2246945	A4GNT	cis	Nerve Tibial	GTEx
rs2246945	A4GNT	cis	Thyroid	GTEx
rs2246945	A4GNT	cis	lung	GTEx
rs2246945	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137834800-137843600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:137835000-137843600	Weak transcription	Right Ventricle	heart
3	chr3:137835200-137843600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:137835200-137843600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr3:137835200-137843600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:137835400-137844200	Weak transcription	A549	lung
7	chr3:137835800-137843600	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr3:137838000-137843600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:137838000-137844600	Weak transcription	Adipose Nuclei	Adipose
10	chr3:137838200-137843600	Weak transcription	Fetal Heart	heart
11	chr3:137838400-137843600	Weak transcription	Fetal Muscle Trunk	muscle
12	chr3:137838400-137843600	Weak transcription	Hela-S3	cervix
13	chr3:137842200-137843600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:137842600-137845800	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr3:137842800-137845400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr3:137843000-137843600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:137843000-137843800	Enhancers	Placenta	Placenta
18	chr3:137843000-137845000	Enhancers	Fetal Muscle Leg	muscle
19	chr3:137843000-137845200	Enhancers	Primary neutrophils fromperipheralblood	blood
20	chr3:137843200-137843800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
21	chr3:137843200-137845000	Enhancers	Primary B cells from cord blood	blood
22	chr3:137843200-137845000	Enhancers	Duodenum Smooth Muscle	Duodenum
23	chr3:137843400-137843600	Enhancers	Osteobl	bone
24	chr3:137843400-137843800	Flanking Active TSS	HSMM	muscle
25	chr3:137843400-137843800	Flanking Active TSS	HSMMtube	muscle
26	chr3:137843400-137844200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:137843400-137845000	Enhancers	Brain Hippocampus Middle	brain

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