Variant report

Variant	rs2638031
Chromosome Location	chr3:112287760-112287761
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr3:112287549-112287760	MCF10A-Er-Src	breast:	n/a	n/a
2	PBX3	chr3:112287407-112287955	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr3:112287462-112287800	SK-N-SH	brain:	n/a	n/a
4	FOSL2	chr3:112287470-112287896	SK-N-SH	brain:	n/a	n/a
5	TCF12	chr3:112287403-112287873	SK-N-SH	brain:	n/a	n/a
6	EP300	chr3:112287495-112287766	SK-N-SH_RA	brain:	n/a	n/a
7	JUND	chr3:112287456-112287990	SK-N-SH	brain:	n/a	n/a
8	FOS	chr3:112287563-112287760	MCF10A-Er-Src	breast:	n/a	n/a
9	PBX3	chr3:112287392-112287970	SK-N-SH	brain:	n/a	n/a
10	EP300	chr3:112287450-112287777	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:112285735..112288489-chr3:112291503..112294225,2	K562	blood:

Variant related genes	Relation type
SLC35A5	TF binding region

Extended variants
information (count: 94 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs11489073	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11706550	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12632867	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs1386895	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs1398091	0.85[GIH][hapmap]
rs1512005	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][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];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1533159	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs1844089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1873571	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]
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];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1994713	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2101632	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2131008	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2171513	0.81[CHB][hapmap]
rs2172196	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2279532	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2280066	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2464611	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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];0.88[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];0.88[ASN][1000 genomes]
rs2633582	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2633584	0.88[ASN][1000 genomes]
rs2638016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638017	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638018	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638019	0.81[CHB][hapmap]
rs2638022	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638023	0.81[CHB][hapmap]
rs2638026	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2638029	0.81[CHB][hapmap]
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];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[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]
rs2638039	0.91[CHB][hapmap]
rs2638042	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638045	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2668217	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2668220	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2668222	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2668223	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[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];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2705521	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2705522	0.81[CHB][hapmap]
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]
rs2705541	0.81[CHB][hapmap]
rs2705543	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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];0.88[ASN][1000 genomes]
rs28866814	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2933134	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2933135	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2933142	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2952319	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2952323	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2952326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2952327	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs2969895	0.80[CHB][hapmap]
rs2969896	0.81[CHB][hapmap];0.90[GIH][hapmap]
rs2971204	0.81[CHB][hapmap]
rs34233684	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732815	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][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	0.81[ASN][1000 genomes]
rs5000995	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6438079	0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap]
rs6774355	0.85[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];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs728568	0.81[CHB][hapmap]
rs7625366	0.84[AMR][1000 genomes]
rs7652377	0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs766968	0.94[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9288952	0.88[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap]
rs9288954	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9756562	0.88[ASN][1000 genomes]
rs9809247	0.84[AMR][1000 genomes]
rs9848054	0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9854043	0.85[ASN][1000 genomes]
rs9866734	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9869455	0.85[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9869579	0.93[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs998036	0.85[GIH][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2638031	SLC35A5	cis	Adipose Subcutaneous	GTEx
rs2638031	SLC35A5	cis	lymphoblastoid	seeQTL
rs2638031	SLC35A5	cis	Artery Tibial	GTEx
rs2638031	SLC35A5	cis	Nerve Tibial	GTEx
rs2638031	SLC35A5	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112281800-112289800	Weak transcription	HSMMtube	muscle
2	chr3:112281800-112290400	Weak transcription	Lung	lung
3	chr3:112281800-112291400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr3:112281800-112299400	Weak transcription	Left Ventricle	heart
5	chr3:112281800-112301600	Weak transcription	HepG2	liver
6	chr3:112281800-112312000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:112281800-112315400	Weak transcription	Pancreas	Pancrea
8	chr3:112281800-112324200	Weak transcription	Spleen	Spleen
9	chr3:112281800-112325400	Weak transcription	Gastric	stomach
10	chr3:112282000-112288200	Weak transcription	Ovary	ovary
11	chr3:112282000-112289600	Weak transcription	Colonic Mucosa	Colon
12	chr3:112282000-112312200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:112282000-112330400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:112282000-112330600	Weak transcription	Esophagus	oesophagus
15	chr3:112282200-112303400	Weak transcription	Psoas Muscle	Psoas
16	chr3:112282400-112288200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr3:112282400-112289000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr3:112282400-112289200	Weak transcription	Brain Substantia Nigra	brain
19	chr3:112282400-112289800	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:112282400-112290400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:112282400-112290400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr3:112282400-112291200	Weak transcription	NHLF	lung
23	chr3:112282400-112291800	Weak transcription	Fetal Kidney	kidney
24	chr3:112282400-112299400	Weak transcription	Fetal Stomach	stomach
25	chr3:112282400-112301600	Weak transcription	Hela-S3	cervix
26	chr3:112282400-112304400	Weak transcription	Fetal Heart	heart
27	chr3:112282400-112306600	Weak transcription	Right Ventricle	heart
28	chr3:112282400-112307200	Weak transcription	Small Intestine	intestine
29	chr3:112282400-112312400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:112282400-112316800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:112282400-112322800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:112282400-112324200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:112282400-112340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:112282600-112288200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr3:112282600-112288200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr3:112282600-112289600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:112282600-112291800	Weak transcription	NHDF-Ad	bronchial
38	chr3:112282600-112297200	Weak transcription	Thymus	Thymus
39	chr3:112282600-112298200	Weak transcription	NHEK	skin
40	chr3:112282600-112301200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:112282600-112301400	Weak transcription	A549	lung
42	chr3:112282600-112306800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:112282800-112289400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr3:112282800-112289600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:112282800-112289600	Weak transcription	Dnd41	blood
46	chr3:112282800-112291400	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:112282800-112292600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr3:112282800-112298600	Weak transcription	Brain Angular Gyrus	brain
49	chr3:112282800-112301400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:112282800-112302200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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