Variant report

Variant	rs4286426
Chromosome Location	chr3:115718820-115718821
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:115718424..115720399-chr3:115727607..115730544,2	K562	blood:
2	chr3:115714015..115716158-chr3:115718030..115720877,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs11918028	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12485818	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs12495426	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs13065579	0.86[JPT][hapmap]
rs13086615	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1920382	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1920383	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs1920384	0.93[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap]
rs1920388	0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2141626	0.86[JPT][hapmap]
rs2141629	0.86[JPT][hapmap]
rs35764849	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4131452	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4131453	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4240163	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4240164	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4240165	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4240166	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4315682	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4378955	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4398428	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.90[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4399891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4426677	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4518124	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs4599302	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4611819	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4831218	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4831219	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4831220	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4831221	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4831222	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4831223	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6438296	1.00[ASW][hapmap];0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.92[MKK][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6776244	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs6777196	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6787687	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787872	1.00[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.81[ASN][1000 genomes]
rs6789600	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790290	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6795318	0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6804278	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6807809	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[YRI][hapmap]
rs7610371	0.93[CHD][hapmap];0.86[JPT][hapmap]
rs7625191	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.84[MEX][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7632252	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9289033	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9289034	0.92[CEU][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9289040	0.90[CHD][hapmap];0.86[JPT][hapmap]
rs9813153	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[ASN][1000 genomes]
rs9815418	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9833319	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9840787	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9848298	1.00[CHD][hapmap];0.82[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs9850406	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9863087	1.00[CHD][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.81[ASN][1000 genomes]
rs9869887	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9872913	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9873260	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9878286	0.86[CHD][hapmap];0.86[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931948	chr3:114884574-115802562	Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2760762	chr3:115476222-115807650	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv829685	chr3:115643521-115812913	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1012260	chr3:115680931-115935968	Enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4286426	B4GALT4	cis	cerebellum	SCAN
rs4286426	POPDC2	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:115717200-115719000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr3:115717200-115719600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:115717400-115720400	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr3:115717800-115719000	Enhancers	iPS-15b Cell Line	embryonic stem cell
5	chr3:115717800-115719000	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr3:115717800-115719200	Enhancers	NHDF-Ad	bronchial
7	chr3:115717800-115719400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:115717800-115719400	Enhancers	Muscle Satellite Cultured Cells	--
9	chr3:115717800-115719400	Weak transcription	Fetal Brain Male	brain
10	chr3:115717800-115719600	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr3:115718000-115719400	Enhancers	NHEK	skin
12	chr3:115718000-115719600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:115718000-115719800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr3:115718000-115720200	Enhancers	HSMMtube	muscle
15	chr3:115718000-115721400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:115718000-115721400	Enhancers	HSMM	muscle
17	chr3:115718200-115719400	Enhancers	Brain Anterior Caudate	brain
18	chr3:115718200-115719600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
19	chr3:115718200-115719600	Enhancers	Fetal Muscle Leg	muscle
20	chr3:115718200-115720000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:115718200-115720000	Enhancers	K562	blood
22	chr3:115718200-115720600	Enhancers	NHLF	lung
23	chr3:115718200-115721800	Enhancers	Osteobl	bone
24	chr3:115718400-115719600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr3:115718400-115719800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:115718400-115720000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr3:115718400-115720000	Enhancers	GM12878-XiMat	blood
28	chr3:115718400-115721200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:115718400-115721400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr3:115718400-115721600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr3:115718400-115721800	Enhancers	HMEC	breast
32	chr3:115718400-115722800	Enhancers	Pancreatic Islets	Pancreatic Islet
33	chr3:115718600-115719200	Enhancers	A549	lung
34	chr3:115718600-115719400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr3:115718600-115719400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:115718600-115719400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr3:115718600-115719400	Enhancers	Brain Hippocampus Middle	brain
38	chr3:115718600-115719800	Enhancers	Hela-S3	cervix
39	chr3:115718600-115721600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr3:115718600-115721600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:115718800-115719000	Enhancers	Brain Substantia Nigra	brain
42	chr3:115718800-115719200	Flanking Active TSS	NH-A	brain
43	chr3:115718800-115719600	Enhancers	Brain Cingulate Gyrus	brain
44	chr3:115718800-115719600	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr3:115718800-115720000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr3:115718800-115721400	Weak transcription	Brain Angular Gyrus	brain

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