Variant report

Variant	rs2638045
Chromosome Location	chr3:112242208-112242209
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10755071	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11489073	0.90[EUR][1000 genomes]
rs1386895	0.80[ASN][1000 genomes]
rs1512005	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1512006	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1844089	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1877363	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1994713	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2101632	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2131008	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2172196	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2279532	0.87[AMR][1000 genomes]
rs2464611	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2633555	0.81[AMR][1000 genomes]
rs2633578	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2633580	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2633582	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2633584	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2638016	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638017	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638018	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638022	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638031	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638037	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638042	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668217	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2668220	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2668222	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2668223	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2705517	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2705531	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2705532	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2705534	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2705543	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2705566	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2933142	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2952323	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2952326	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2952327	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34233684	0.83[AMR][1000 genomes]
rs4682413	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5000995	0.94[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6772077	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6774355	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6792947	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7625366	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7652377	0.83[AMR][1000 genomes]
rs766968	0.80[AMR][1000 genomes]
rs9756562	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9809247	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9848054	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854043	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9869455	0.83[AMR][1000 genomes]
rs9869579	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
7	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv965197	chr3:112238965-112250194	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2638045	SLC35A5	cis	Nerve Tibial	GTEx
rs2638045	SLC35A5	cis	Thyroid	GTEx
rs2638045	SLC35A5	cis	Adipose Subcutaneous	GTEx
rs2638045	SLC35A5	cis	Artery Tibial	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112227400-112269800	Weak transcription	Small Intestine	intestine
2	chr3:112231600-112246800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr3:112234000-112247600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr3:112234200-112272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr3:112235600-112243000	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr3:112237000-112245400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr3:112237000-112247000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:112237200-112245600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr3:112237200-112247400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr3:112237200-112254200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr3:112237400-112245400	Weak transcription	Primary B cells from cord blood	blood
12	chr3:112237600-112242600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:112237800-112245200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:112238000-112245800	Weak transcription	Primary T cells from cord blood	blood
15	chr3:112238200-112245600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:112238200-112245800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:112238200-112247000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr3:112238200-112247400	Weak transcription	GM12878-XiMat	blood
19	chr3:112238600-112245800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:112238600-112249200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:112238800-112242400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:112238800-112245600	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:112238800-112246000	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:112239000-112243200	Weak transcription	Fetal Stomach	stomach
25	chr3:112239400-112242400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr3:112239600-112272200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:112239800-112245800	Weak transcription	Brain Germinal Matrix	brain
28	chr3:112239800-112247200	Weak transcription	Lung	lung
29	chr3:112239800-112247400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:112239800-112247800	Weak transcription	Aorta	Aorta
31	chr3:112239800-112247800	Weak transcription	Esophagus	oesophagus
32	chr3:112240000-112245800	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr3:112240400-112243000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr3:112240400-112243000	Weak transcription	Left Ventricle	heart
35	chr3:112240400-112245800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr3:112240600-112243200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr3:112240600-112246600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr3:112240800-112242400	Weak transcription	Brain Anterior Caudate	brain
39	chr3:112240800-112242600	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr3:112241000-112242800	Weak transcription	Adipose Nuclei	Adipose
41	chr3:112241000-112246400	Weak transcription	Fetal Muscle Leg	muscle
42	chr3:112241000-112251600	Weak transcription	HUVEC	blood vessel
43	chr3:112241200-112242800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:112241200-112243000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr3:112241200-112243000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:112241200-112245400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr3:112241200-112245800	Weak transcription	Brain Angular Gyrus	brain
48	chr3:112241400-112243600	Weak transcription	Pancreas	Pancrea
49	chr3:112241400-112245000	Weak transcription	Liver	Liver
50	chr3:112241400-112245600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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