Variant report

Variant	rs2638042
Chromosome Location	chr3:112247109-112247110
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	POLR2A	chr3:112247074-112248291	K562	blood:	n/a	n/a

Variant related genes	Relation type
OR7E100P	TF binding region

Extended variants
information (count: 68 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10755071	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11489073	0.92[EUR][1000 genomes]
rs11706550	0.82[EUR][1000 genomes]
rs1386895	0.80[ASN][1000 genomes]
rs1512005	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1512006	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1844089	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1877363	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1994713	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2101632	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2131008	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2172196	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2279532	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2280066	0.82[EUR][1000 genomes]
rs2464611	0.84[AMR][1000 genomes];0.94[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];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638017	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638018	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638022	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2638031	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2638037	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2638045	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2668217	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2668220	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2668222	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2668223	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2705517	0.96[EUR][1000 genomes];0.85[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	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2705566	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs28866814	0.82[EUR][1000 genomes]
rs2933142	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2952323	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2952326	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2952327	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34233684	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3732815	0.82[EUR][1000 genomes]
rs4682413	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5000995	0.94[AMR][1000 genomes];0.82[EUR][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];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7652377	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs766968	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9288954	0.82[EUR][1000 genomes]
rs9756562	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs9809247	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9848054	0.97[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9854043	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9866734	0.82[EUR][1000 genomes]
rs9869455	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9869579	0.83[AMR][1000 genomes];0.82[EUR][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
rs2638042	SLC35A5	cis	Artery Tibial	GTEx
rs2638042	SLC35A5	cis	Thyroid	GTEx
rs2638042	SLC35A5	cis	Nerve Tibial	GTEx
rs2638042	SLC35A5	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:118 , 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	chr3:112234000-112247600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr3:112234200-112272000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:112237200-112247400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:112237200-112254200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr3:112238200-112247400	Weak transcription	GM12878-XiMat	blood
7	chr3:112238600-112249200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:112239600-112272200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:112239800-112247200	Weak transcription	Lung	lung
10	chr3:112239800-112247400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:112239800-112247800	Weak transcription	Aorta	Aorta
12	chr3:112239800-112247800	Weak transcription	Esophagus	oesophagus
13	chr3:112241000-112251600	Weak transcription	HUVEC	blood vessel
14	chr3:112241600-112259400	Strong transcription	Monocytes-CD14+_RO01746	blood
15	chr3:112242000-112247400	Weak transcription	Spleen	Spleen
16	chr3:112242000-112247800	Weak transcription	Gastric	stomach
17	chr3:112242000-112248400	Weak transcription	NHDF-Ad	bronchial
18	chr3:112242200-112247400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:112242200-112247600	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:112242200-112248000	Weak transcription	Fetal Intestine Small	intestine
21	chr3:112242200-112252200	Weak transcription	NHLF	lung
22	chr3:112242400-112247800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr3:112242400-112247800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr3:112242400-112249800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:112242600-112263800	Strong transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:112243000-112271600	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr3:112243400-112247400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr3:112243600-112247200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr3:112244000-112247400	Weak transcription	Brain Anterior Caudate	brain
30	chr3:112244000-112259800	Weak transcription	Pancreas	Pancrea
31	chr3:112244200-112247400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr3:112244200-112247600	Weak transcription	Fetal Lung	lung
33	chr3:112244200-112251200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:112244400-112247400	Weak transcription	Colonic Mucosa	Colon
35	chr3:112244400-112274200	Weak transcription	Stomach Mucosa	stomach
36	chr3:112244400-112278200	Weak transcription	K562	blood
37	chr3:112244400-112278400	Weak transcription	HSMMtube	muscle
38	chr3:112244600-112247200	Weak transcription	HMEC	breast
39	chr3:112244600-112256200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:112244600-112264800	Weak transcription	NHEK	skin
41	chr3:112245000-112249600	Strong transcription	Liver	Liver
42	chr3:112245000-112249800	Strong transcription	Adipose Nuclei	Adipose
43	chr3:112245200-112263200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr3:112245200-112273200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr3:112245400-112247200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr3:112245400-112248200	Strong transcription	Fetal Brain Female	brain
47	chr3:112245400-112248400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
48	chr3:112245400-112248600	Strong transcription	Primary B cells from cord blood	blood
49	chr3:112245400-112262800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr3:112245600-112247800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain

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