Variant report

Variant	rs9827617
Chromosome Location	chr3:137879108-137879109
allele	G/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	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11712078	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12185936	0.88[ASN][1000 genomes]
rs12185998	0.84[ASN][1000 genomes]
rs1600697	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2170309	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs2219936	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2246945	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs2251550	0.80[EUR][1000 genomes]
rs2346744	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2346745	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2346747	0.95[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs2622694	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622695	0.81[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2622696	0.83[ASN][1000 genomes]
rs2622699	0.80[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];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622732	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2622733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2622734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2622736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622737	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2622739	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622740	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2622741	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2622742	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622743	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2622744	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2724681	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2724690	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2724691	0.95[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2724692	0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2724710	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2724711	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2724712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2724725	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2724726	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2724727	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs329380	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3732839	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs608594	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7430414	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7613041	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7613558	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7632402	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs774803	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs774804	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs774805	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs774806	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs774807	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774808	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774809	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774810	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774811	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774812	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774813	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs774814	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.87[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs811810	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs811811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.87[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9840008	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9851548	0.89[AMR][1000 genomes];0.99[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
rs9827617	A4GNT	cis	Adipose Subcutaneous	GTEx
rs9827617	DBR1	cis	normal skin	skin_eQTL
rs9827617	A4GNT	cis	lung	GTEx
rs9827617	A4GNT	cis	Thyroid	GTEx
rs9827617	A4GNT	cis	Nerve Tibial	GTEx
rs9827617	A4GNT	cis	Artery Tibial	GTEx
rs9827617	A4GNT	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:137876000-137879200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr3:137876000-137880000	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:137876000-137880000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr3:137876000-137880400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:137876000-137884800	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:137876000-137892400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr3:137876400-137892800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:137876600-137879200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:137876800-137879200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:137876800-137879200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:137877000-137879200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:137877200-137879200	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr3:137877200-137879200	Weak transcription	Left Ventricle	heart
14	chr3:137877200-137879400	Weak transcription	Brain Germinal Matrix	brain
15	chr3:137877200-137879800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:137877200-137880400	Weak transcription	Brain Cingulate Gyrus	brain
17	chr3:137877200-137880600	Weak transcription	Psoas Muscle	Psoas
18	chr3:137877200-137880600	Weak transcription	HUVEC	blood vessel
19	chr3:137877200-137882000	Weak transcription	NHDF-Ad	bronchial
20	chr3:137877200-137882800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr3:137877400-137879200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:137877400-137879200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:137877400-137879200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr3:137877400-137879200	Weak transcription	Liver	Liver
25	chr3:137877400-137879400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:137877400-137880000	Weak transcription	Primary B cells from cord blood	blood
27	chr3:137877400-137880000	Weak transcription	Primary B cells from peripheral blood	blood
28	chr3:137877400-137880400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr3:137877400-137880600	Weak transcription	Dnd41	blood
30	chr3:137877400-137880800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr3:137877600-137879200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:137877600-137879200	Weak transcription	Primary T cells from cord blood	blood
33	chr3:137877600-137879200	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr3:137877600-137879200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr3:137877600-137879200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:137877600-137879200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr3:137877600-137879200	Weak transcription	Adipose Nuclei	Adipose
38	chr3:137877600-137879200	Weak transcription	Fetal Intestine Large	intestine
39	chr3:137877600-137879200	Weak transcription	Fetal Lung	lung
40	chr3:137877600-137879200	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:137877600-137879200	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:137877600-137879200	Weak transcription	HSMMtube	muscle
43	chr3:137877600-137879600	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:137877600-137879800	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr3:137877600-137880400	Weak transcription	Right Ventricle	heart
46	chr3:137877600-137880800	Weak transcription	Ovary	ovary
47	chr3:137877600-137880800	Weak transcription	Osteobl	bone
48	chr3:137877800-137879400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:137877800-137879400	Weak transcription	Fetal Stomach	stomach
50	chr3:137877800-137879400	Weak transcription	Lung	lung

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