Variant report

Variant	rs3732815
Chromosome Location	chr3:112316935-112316936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLC35A5-1	chr3:112315667-112322287	XLOC_002759
2	lnc-CCDC80-2	chr3:112315703-112318342	NONHSAT091188
3	lnc-CCDC80-2	chr3:112315641-112320816	NR_109779
4	lnc-CCDC80-2	chr3:112315641-112320749	ENSG00000272761.1

Extended variants
information (count: 56 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10755071	0.84[ASN][1000 genomes]
rs11489073	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11706550	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512005	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1512006	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1844089	0.89[EUR][1000 genomes]
rs1877363	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1994713	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2101632	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2131008	0.82[EUR][1000 genomes]
rs2172196	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279532	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2280066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2464611	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2633555	0.84[EUR][1000 genomes]
rs2633578	0.87[EUR][1000 genomes]
rs2633580	0.87[EUR][1000 genomes]
rs2633582	0.89[EUR][1000 genomes]
rs2633584	0.86[EUR][1000 genomes]
rs2638016	0.82[EUR][1000 genomes]
rs2638022	0.82[EUR][1000 genomes]
rs2638031	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2638042	0.82[EUR][1000 genomes]
rs2668217	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2668220	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2668222	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2668223	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2705517	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2705531	0.89[EUR][1000 genomes]
rs2705532	0.83[EUR][1000 genomes]
rs2705534	0.89[EUR][1000 genomes]
rs2705543	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2705566	0.87[EUR][1000 genomes]
rs28866814	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2933142	0.81[ASN][1000 genomes]
rs2952323	0.91[EUR][1000 genomes]
rs34233684	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4682413	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5000995	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6772077	0.81[ASN][1000 genomes]
rs6774355	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6792947	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7625366	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7652377	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs766968	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9288954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9756562	0.89[EUR][1000 genomes]
rs9809247	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9848054	0.81[AFR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9854043	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9866734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9869455	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9869579	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3732815	SLC35A5	cis	Nerve Tibial	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
2	chr3:112281800-112325400	Weak transcription	Gastric	stomach
3	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
5	chr3:112282400-112322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:112282400-112324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:112290400-112317400	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr3:112291600-112320600	Weak transcription	NHLF	lung
10	chr3:112293200-112318000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:112298600-112325200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:112298800-112335200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:112300200-112317400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:112300200-112331000	Weak transcription	Lung	lung
15	chr3:112300200-112334000	Weak transcription	Fetal Stomach	stomach
16	chr3:112302000-112317400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr3:112302600-112322800	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:112302800-112324200	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr3:112303400-112317000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:112303600-112322800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr3:112303800-112324200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr3:112304000-112320400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr3:112304200-112317600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr3:112305000-112324200	Weak transcription	Fetal Brain Male	brain
25	chr3:112305200-112317200	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr3:112305200-112323000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:112305200-112323600	Weak transcription	Brain Substantia Nigra	brain
28	chr3:112305400-112323400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:112305400-112324000	Weak transcription	Brain Anterior Caudate	brain
30	chr3:112305400-112330400	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:112305600-112324200	Weak transcription	Fetal Kidney	kidney
32	chr3:112305800-112334800	Weak transcription	Aorta	Aorta
33	chr3:112307400-112329000	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:112309800-112318200	Weak transcription	Placenta	Placenta
35	chr3:112311600-112330600	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr3:112311600-112331000	Weak transcription	Psoas Muscle	Psoas
37	chr3:112312200-112317400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr3:112312200-112317600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr3:112312200-112318000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr3:112312400-112324200	Weak transcription	Ovary	ovary
41	chr3:112312400-112325200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:112312400-112326800	Weak transcription	Fetal Lung	lung
43	chr3:112312400-112331000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr3:112312600-112317200	Weak transcription	Fetal Brain Female	brain
45	chr3:112312600-112317400	Weak transcription	Thymus	Thymus
46	chr3:112312600-112317800	Weak transcription	Primary B cells from peripheral blood	blood
47	chr3:112312600-112318400	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr3:112312600-112322000	Weak transcription	HUVEC	blood vessel
49	chr3:112312600-112323000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:112312600-112323400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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