Variant report

Variant	rs2705543
Chromosome Location	chr3:112315222-112315223
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11489073	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11706550	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1512005	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1512006	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1844089	0.80[ASN][1000 genomes]
rs1877363	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1994713	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2101632	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131008	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2172196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2279532	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2280066	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2464611	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2633578	0.80[ASN][1000 genomes]
rs2633580	0.80[ASN][1000 genomes]
rs2633582	0.80[ASN][1000 genomes]
rs2633584	0.80[ASN][1000 genomes]
rs2638016	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638017	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638018	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638022	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638031	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638037	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638042	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638045	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2668217	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668222	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668223	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2705517	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2705566	0.80[ASN][1000 genomes]
rs28866814	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2933142	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2952323	0.80[ASN][1000 genomes]
rs2952326	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2952327	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34233684	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3732815	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682413	0.81[ASN][1000 genomes]
rs5000995	0.83[EUR][1000 genomes]
rs6792947	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7652377	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs766968	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9288954	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9756562	0.80[ASN][1000 genomes]
rs9848054	0.81[ASN][1000 genomes]
rs9866734	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9869455	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9869579	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv591301	chr3:112252532-112332629	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2705543	SLC35A5	cis	Adipose Subcutaneous	GTEx
rs2705543	SLC35A5	cis	Artery Tibial	GTEx
rs2705543	SLC35A5	cis	Thyroid	GTEx
rs2705543	SLC35A5	cis	Nerve Tibial	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112281800-112315400	Weak transcription	Pancreas	Pancrea
2	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
3	chr3:112281800-112325400	Weak transcription	Gastric	stomach
4	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
6	chr3:112282400-112316800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:112282400-112322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr3:112282400-112324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr3:112283000-112316400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:112290400-112317400	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:112290600-112315600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr3:112291600-112320600	Weak transcription	NHLF	lung
14	chr3:112293200-112315600	Weak transcription	NH-A	brain
15	chr3:112293200-112318000	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr3:112298600-112325200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:112298800-112335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:112300200-112315800	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr3:112300200-112317400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr3:112300200-112331000	Weak transcription	Lung	lung
21	chr3:112300200-112334000	Weak transcription	Fetal Stomach	stomach
22	chr3:112301600-112315600	Weak transcription	Stomach Mucosa	stomach
23	chr3:112301600-112316600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr3:112302000-112317400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr3:112302600-112322800	Weak transcription	Colon Smooth Muscle	Colon
26	chr3:112302800-112324200	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:112303400-112317000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:112303600-112322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:112303800-112324200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:112304000-112320400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:112304200-112317600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:112305000-112324200	Weak transcription	Fetal Brain Male	brain
33	chr3:112305200-112315400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr3:112305200-112315600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr3:112305200-112315800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:112305200-112316000	Weak transcription	Osteobl	bone
37	chr3:112305200-112317200	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr3:112305200-112323000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr3:112305200-112323600	Weak transcription	Brain Substantia Nigra	brain
40	chr3:112305400-112323400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr3:112305400-112324000	Weak transcription	Brain Anterior Caudate	brain
42	chr3:112305400-112330400	Weak transcription	Skeletal Muscle Female	skeletal muscle
43	chr3:112305600-112324200	Weak transcription	Fetal Kidney	kidney
44	chr3:112305800-112334800	Weak transcription	Aorta	Aorta
45	chr3:112306800-112315800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:112307400-112329000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:112309600-112315600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:112309800-112318200	Weak transcription	Placenta	Placenta
49	chr3:112311400-112316800	Strong transcription	Primary T cells from cord blood	blood
50	chr3:112311600-112316600	Strong transcription	Monocytes-CD14+_RO01746	blood

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