Variant report

Variant	rs1440228
Chromosome Location	chr4:47890838-47890839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 75 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10002500	0.91[YRI][hapmap]
rs10008818	0.85[CEU][hapmap]
rs10025104	0.80[JPT][hapmap]
rs10028155	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10030927	0.81[JPT][hapmap]
rs10049713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1012844	0.85[CEU][hapmap]
rs1062858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10938499	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10938500	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10938504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10938505	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10938506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12186152	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12504018	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12506632	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12507439	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12510002	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12641871	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12651301	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1371729	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1371731	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1440221	0.83[EUR][1000 genomes]
rs1440227	0.81[JPT][hapmap]
rs16860663	0.82[EUR][1000 genomes]
rs17463666	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17573709	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1822030	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1866689	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1984713	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2033893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2053404	0.80[JPT][hapmap]
rs2289433	0.80[JPT][hapmap]
rs2289435	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2352470	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2661513	0.95[YRI][hapmap]
rs28395298	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28412313	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28460483	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28573115	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28583602	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28636596	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3113881	0.87[YRI][hapmap]
rs321623	0.82[YRI][hapmap]
rs4529019	0.81[JPT][hapmap]
rs4565052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4695303	0.80[JPT][hapmap]
rs4695306	0.80[JPT][hapmap]
rs56001837	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6414687	0.80[JPT][hapmap]
rs6447586	0.81[JPT][hapmap]
rs6447587	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6447589	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6447593	0.81[JPT][hapmap]
rs6811177	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6818556	0.80[JPT][hapmap]
rs6823184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6823698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6833758	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6844286	0.81[JPT][hapmap]
rs6858440	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8180146	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9291317	0.80[JPT][hapmap]
rs978094	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9994561	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9995122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9997555	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][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	nsv1008515	chr4:47488431-47906835	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv948568	chr4:47488431-47907524	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv1004939	chr4:47488573-47901460	Bivalent Enhancer Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv537080	chr4:47488573-47901460	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv997471	chr4:47489412-47895223	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1000337	chr4:47493907-47902019	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv594118	chr4:47560386-47917730	Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
8	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1440228	NFXL1	cis	Whole Blood	GTEx
rs1440228	CNGA1	cis	Heart Left Ventricle	GTEx
rs1440228	CNGA1	cis	Adipose Subcutaneous	GTEx
rs1440228	CORIN	cis	Whole Blood	GTEx
rs1440228	RP11-121C2.2	cis	Whole Blood	GTEx
rs1440228	CNGA1	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:47843800-47897000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr4:47861200-47893200	Weak transcription	Gastric	stomach
3	chr4:47865400-47913400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr4:47865600-47894000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:47872400-47911600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr4:47873400-47913400	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr4:47873600-47910600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:47874400-47913400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
9	chr4:47874400-47913600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr4:47875800-47903000	Strong transcription	Dnd41	blood
11	chr4:47876000-47893800	Weak transcription	Colonic Mucosa	Colon
12	chr4:47876000-47906200	Weak transcription	Spleen	Spleen
13	chr4:47876000-47908600	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr4:47876000-47915200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:47876200-47900800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr4:47876200-47915200	Weak transcription	Right Ventricle	heart
17	chr4:47876400-47915200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr4:47876600-47905400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:47876800-47893800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:47876800-47915800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr4:47877200-47891200	Weak transcription	Brain Germinal Matrix	brain
22	chr4:47877400-47895600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:47877400-47906000	Weak transcription	Esophagus	oesophagus
24	chr4:47877400-47913800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr4:47877600-47913600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr4:47877800-47910200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr4:47879000-47894000	Weak transcription	Fetal Brain Male	brain
28	chr4:47880600-47893400	Weak transcription	Fetal Heart	heart
29	chr4:47880800-47894200	Weak transcription	Brain Angular Gyrus	brain
30	chr4:47881000-47897000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr4:47882200-47891400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr4:47882200-47915200	Weak transcription	Stomach Mucosa	stomach
33	chr4:47882800-47913000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr4:47883000-47902200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:47883000-47902400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr4:47883200-47913600	Strong transcription	HMEC	breast
37	chr4:47883200-47913800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr4:47883200-47914400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr4:47883400-47904400	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:47883800-47902600	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr4:47884200-47913000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr4:47885000-47894600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr4:47885400-47891800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:47886200-47891200	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr4:47886200-47891600	Weak transcription	Primary B cells from cord blood	blood
46	chr4:47886200-47893200	Weak transcription	NHLF	lung
47	chr4:47886200-47893800	Weak transcription	Brain Hippocampus Middle	brain
48	chr4:47886200-47894000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr4:47886200-47894200	Weak transcription	Rectal Smooth Muscle	rectum
50	chr4:47886200-47898000	Weak transcription	Primary T killer memory cells from peripheral blood	blood

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