Variant report

Variant	rs2170309
Chromosome Location	chr3:137843106-137843107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 132 )
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];0.85[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];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs179282	0.87[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2219936	0.86[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2246945	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]
rs2346747	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs2622694	0.86[CEU][hapmap];0.83[MEX][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];0.90[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];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2622718	0.86[ASN][1000 genomes]
rs2622719	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2622720	0.82[CHB][hapmap];0.91[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[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2724693	0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2724694	0.88[ASN][1000 genomes]
rs2724697	0.82[CHB][hapmap];0.91[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];0.91[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];0.93[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];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs329390	0.93[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs329391	0.93[CHB][hapmap];0.88[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];0.93[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];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs425938	0.83[ASN][1000 genomes]
rs442800	0.82[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs445025	0.83[ASN][1000 genomes]
rs446644	0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs452195	0.80[ASN][1000 genomes]
rs453023	0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4678403	0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[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];0.90[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];0.91[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	0.93[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][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: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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2170309	A4GNT	cis	lung	GTEx
rs2170309	A4GNT	cis	Artery Tibial	GTEx
rs2170309	A4GNT	cis	Thyroid	GTEx
rs2170309	A4GNT	cis	Nerve Tibial	GTEx
rs2170309	DBR1	Cis_1M	lymphoblastoid	RTeQTL
rs2170309	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:23 , 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	chr3:137835200-137843200	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr3:137835200-137843600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:137835200-137843600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr3:137835200-137843600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:137835400-137843400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr3:137835400-137844200	Weak transcription	A549	lung
9	chr3:137835800-137843600	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr3:137838000-137843400	Weak transcription	Osteobl	bone
11	chr3:137838000-137843600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:137838000-137844600	Weak transcription	Adipose Nuclei	Adipose
13	chr3:137838200-137843600	Weak transcription	Fetal Heart	heart
14	chr3:137838400-137843600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr3:137838400-137843600	Weak transcription	Hela-S3	cervix
16	chr3:137842200-137843600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:137842600-137845800	Enhancers	Primary monocytes fromperipheralblood	blood
18	chr3:137842800-137845400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr3:137843000-137843400	ZNF genes & repeats	HSMM	muscle
20	chr3:137843000-137843600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr3:137843000-137843800	Enhancers	Placenta	Placenta
22	chr3:137843000-137845000	Enhancers	Fetal Muscle Leg	muscle
23	chr3:137843000-137845200	Enhancers	Primary neutrophils fromperipheralblood	blood

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