Variant report

Variant	rs1873571
Chromosome Location	chr3:112259388-112259389
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10755071	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11489073	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12632867	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1386895	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs1398091	0.85[GIH][hapmap]
rs1512005	0.81[AMR][1000 genomes]
rs1512006	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes]
rs1533159	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs1844089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1873572	0.81[CHB][hapmap]
rs1877363	0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes]
rs1994713	0.81[AMR][1000 genomes]
rs2101632	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2131008	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2171513	0.81[CHB][hapmap]
rs2172196	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2279532	0.86[AMR][1000 genomes]
rs2464611	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2633555	0.80[AMR][1000 genomes]
rs2633574	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2633578	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2633579	0.81[CHB][hapmap]
rs2633580	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2633582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2633584	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2638016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638018	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638019	0.81[CHB][hapmap]
rs2638022	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2638023	0.81[CHB][hapmap]
rs2638026	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2638029	0.81[CHB][hapmap]
rs2638031	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638032	0.81[CHB][hapmap]
rs2638035	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2638037	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638039	0.91[CHB][hapmap]
rs2638042	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638045	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2668217	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2668220	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2668222	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2668223	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2705507	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2705517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2705521	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2705522	0.81[CHB][hapmap]
rs2705531	0.80[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2705532	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2705534	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2705541	0.81[CHB][hapmap]
rs2705543	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2705544	0.81[CHB][hapmap]
rs2705556	0.81[CHB][hapmap]
rs2705559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2705562	0.81[CHB][hapmap]
rs2705565	0.81[CHB][hapmap]
rs2705566	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2933134	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2933135	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2933142	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2952319	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2952323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2952326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2952327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2969895	0.80[CHB][hapmap]
rs2969896	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2971204	0.81[CHB][hapmap]
rs34233684	0.81[AMR][1000 genomes]
rs3846050	1.00[CEU][hapmap]
rs4682410	0.94[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs4682413	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5000995	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6438079	0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap]
rs6772077	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6774355	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6792947	0.94[CHB][hapmap];0.92[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs728568	0.81[CHB][hapmap]
rs7625366	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7652377	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs766968	0.94[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs9288952	0.88[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs9756562	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9809247	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9848054	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9854043	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9866734	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs9869455	0.85[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes]
rs9869579	0.93[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes]
rs998036	0.85[GIH][hapmap]

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	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1873571	SLC35A5	cis	Nerve Tibial	GTEx
rs1873571	SLC35A5	cis	Adipose Subcutaneous	GTEx
rs1873571	SLC35A5	cis	multi-tissue	Pritchard
rs1873571	SLC35A5	cis	Artery Tibial	GTEx
rs1873571	SLC35A5	cis	lymphoblastoid	seeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112227400-112269800	Weak transcription	Small Intestine	intestine
2	chr3:112234200-112272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:112239600-112272200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:112241600-112259400	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr3:112242600-112263800	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr3:112243000-112271600	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:112244000-112259800	Weak transcription	Pancreas	Pancrea
8	chr3:112244400-112274200	Weak transcription	Stomach Mucosa	stomach
9	chr3:112244400-112278200	Weak transcription	K562	blood
10	chr3:112244400-112278400	Weak transcription	HSMMtube	muscle
11	chr3:112244600-112264800	Weak transcription	NHEK	skin
12	chr3:112245200-112263200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:112245200-112273200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr3:112245400-112262800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:112245800-112261400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:112245800-112261800	Strong transcription	Dnd41	blood
17	chr3:112245800-112279600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:112246200-112264600	Weak transcription	Fetal Heart	heart
19	chr3:112247000-112267800	Strong transcription	Rectal Mucosa Donor 29	rectum
20	chr3:112247200-112261000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:112247600-112279600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr3:112247800-112265800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr3:112248000-112264800	Weak transcription	Ovary	ovary
24	chr3:112248200-112264200	Weak transcription	Fetal Brain Female	brain
25	chr3:112248200-112264800	Weak transcription	HepG2	liver
26	chr3:112248400-112259600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:112248400-112265600	Weak transcription	Brain Germinal Matrix	brain
28	chr3:112248400-112266200	Weak transcription	Brain Anterior Caudate	brain
29	chr3:112248400-112274200	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:112248800-112265000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:112249000-112263600	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:112249000-112264800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr3:112249000-112265400	Weak transcription	Right Ventricle	heart
34	chr3:112249200-112265000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:112249200-112265800	Weak transcription	H1 Cell Line	embryonic stem cell
36	chr3:112249200-112269800	Weak transcription	Psoas Muscle	Psoas
37	chr3:112249200-112275800	Weak transcription	Fetal Stomach	stomach
38	chr3:112249200-112276000	Weak transcription	Spleen	Spleen
39	chr3:112249200-112278200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr3:112249200-112278400	Weak transcription	Aorta	Aorta
41	chr3:112249200-112279600	Weak transcription	Esophagus	oesophagus
42	chr3:112249200-112279600	Weak transcription	Gastric	stomach
43	chr3:112249200-112279800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:112249400-112264600	Weak transcription	Thymus	Thymus
45	chr3:112249400-112270000	Weak transcription	Fetal Intestine Small	intestine
46	chr3:112249400-112276200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr3:112249400-112279600	Weak transcription	Lung	lung
48	chr3:112249600-112264600	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:112249600-112265000	Weak transcription	Colonic Mucosa	Colon
50	chr3:112250800-112260600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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