Variant report

Variant	rs2622737
Chromosome Location	chr3:137879993-137879994
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1137760	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11712078	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12185936	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12185998	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1600697	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2170309	0.81[CEU][hapmap]
rs2219936	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2246945	0.81[CEU][hapmap]
rs2251550	0.82[EUR][1000 genomes]
rs2346744	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2346745	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2346747	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622694	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622695	0.81[CEU][hapmap]
rs2622696	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622699	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622700	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622732	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2622733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2622734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622735	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2622736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622739	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622740	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622741	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622742	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622743	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622744	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2724681	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2724690	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724691	0.95[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2724692	0.95[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.86[YRI][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2724710	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2724711	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2724712	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2724725	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2724726	0.95[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2724727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs329380	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608594	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7430414	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7613041	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7613558	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7632402	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs774803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs774804	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs774805	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs774806	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs774807	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774808	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774809	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774810	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774811	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774812	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774813	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774814	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs811810	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs811811	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9827617	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9840008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9851548	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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
7	nsv877536	chr3:137870523-137970907	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2622737	A4GNT	cis	lung	GTEx
rs2622737	A4GNT	cis	Thyroid	GTEx
rs2622737	A4GNT	cis	Adipose Subcutaneous	GTEx
rs2622737	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx
rs2622737	DBR1	Cis_1M	lymphoblastoid	RTeQTL
rs2622737	A4GNT	cis	Nerve Tibial	GTEx
rs2622737	A4GNT	cis	Artery Tibial	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137876000-137880000	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr3:137876000-137880000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr3:137876000-137880400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:137876000-137884800	Weak transcription	Colon Smooth Muscle	Colon
5	chr3:137876000-137892400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr3:137876400-137892800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:137877200-137880400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:137877200-137880600	Weak transcription	Psoas Muscle	Psoas
9	chr3:137877200-137880600	Weak transcription	HUVEC	blood vessel
10	chr3:137877200-137882000	Weak transcription	NHDF-Ad	bronchial
11	chr3:137877200-137882800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr3:137877400-137880000	Weak transcription	Primary B cells from cord blood	blood
13	chr3:137877400-137880000	Weak transcription	Primary B cells from peripheral blood	blood
14	chr3:137877400-137880400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:137877400-137880600	Weak transcription	Dnd41	blood
16	chr3:137877400-137880800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr3:137877600-137880400	Weak transcription	Right Ventricle	heart
18	chr3:137877600-137880800	Weak transcription	Ovary	ovary
19	chr3:137877600-137880800	Weak transcription	Osteobl	bone
20	chr3:137877800-137880200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr3:137877800-137880400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr3:137877800-137880600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:137877800-137880600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr3:137877800-137880600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr3:137877800-137880600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr3:137877800-137880600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:137877800-137880600	Weak transcription	Small Intestine	intestine
28	chr3:137877800-137880600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr3:137877800-137880600	Weak transcription	HepG2	liver
30	chr3:137877800-137880800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr3:137877800-137880800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:137877800-137880800	Weak transcription	Placenta	Placenta
33	chr3:137877800-137880800	Weak transcription	NH-A	brain
34	chr3:137878000-137880200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr3:137878000-137880400	Weak transcription	Aorta	Aorta
36	chr3:137878000-137880600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:137878000-137880600	Weak transcription	Spleen	Spleen
38	chr3:137878000-137880800	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr3:137878000-137880800	Weak transcription	HSMM	muscle
40	chr3:137878000-137885600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:137878200-137880800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr3:137878600-137880400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:137878600-137880400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:137878600-137880400	Weak transcription	Fetal Thymus	thymus
45	chr3:137878600-137880600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:137878600-137880600	Weak transcription	NHEK	skin
47	chr3:137878800-137880600	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:137878800-137880600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:137878800-137880600	Weak transcription	Brain Angular Gyrus	brain
50	chr3:137878800-137880600	Weak transcription	Brain Inferior Temporal Lobe	brain

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