Variant report

Variant	rs1883900
Chromosome Location	chr6:37630995-37630996
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10807186	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12195277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs13198513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13199974	0.98[ASN][1000 genomes]
rs13203140	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13204070	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13212859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1738456	0.92[ASN][1000 genomes]
rs1883899	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2273109	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2273110	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3846873	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3846874	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3846876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3846879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3857567	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3857568	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3857570	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3857571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4236056	1.00[CEU][hapmap];0.92[JPT][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4357132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4711509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6906090	0.92[ASN][1000 genomes]
rs6930085	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs708020	0.92[ASN][1000 genomes]
rs708021	0.92[ASN][1000 genomes]
rs708022	0.92[ASN][1000 genomes]
rs7452633	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7452676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7452692	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs761413	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7775837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs804816	0.92[ASN][1000 genomes]
rs804817	0.93[ASN][1000 genomes]
rs804830	0.82[JPT][hapmap]
rs804831	0.80[CEU][hapmap];0.81[CHB][hapmap];0.84[JPT][hapmap]
rs804859	0.88[CEU][hapmap];0.83[JPT][hapmap]
rs813079	0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9366945	0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9369015	0.92[ASN][1000 genomes]
rs9394447	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9462343	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]

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	esv2752124	chr6:37416219-37680622	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1028825	chr6:37495154-38278320	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv1024016	chr6:37567651-37981590	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1883900	MDGA1	cis	Esophagus Mucosa	GTEx
rs1883900	MDGA1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37618200-37631600	Weak transcription	Gastric	stomach
2	chr6:37620200-37632200	Weak transcription	Right Atrium	heart
3	chr6:37621600-37631400	Weak transcription	Fetal Brain Male	brain
4	chr6:37622400-37632400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr6:37622400-37633000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:37626000-37633400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:37626000-37635000	Weak transcription	A549	lung
8	chr6:37626400-37631400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr6:37626600-37631000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:37627000-37631200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr6:37629000-37631600	Strong transcription	Stomach Smooth Muscle	stomach
12	chr6:37629200-37631000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr6:37629200-37631000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:37629200-37631000	Weak transcription	Brain Substantia Nigra	brain
15	chr6:37629200-37631200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr6:37629200-37632000	Weak transcription	Pancreas	Pancrea
17	chr6:37629200-37635000	Weak transcription	Aorta	Aorta
18	chr6:37629400-37631200	Weak transcription	NHDF-Ad	bronchial
19	chr6:37629400-37646000	Weak transcription	Primary B cells from peripheral blood	blood
20	chr6:37629600-37631400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr6:37629600-37641000	Weak transcription	Fetal Brain Female	brain
22	chr6:37629600-37659600	Weak transcription	Ovary	ovary
23	chr6:37629800-37631200	Weak transcription	Brain Germinal Matrix	brain
24	chr6:37630400-37632800	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr6:37630400-37634600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr6:37630600-37631400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr6:37630600-37631400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr6:37630600-37631600	Enhancers	Fetal Kidney	kidney
29	chr6:37630600-37631800	Enhancers	NHLF	lung
30	chr6:37630600-37633600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr6:37630600-37633800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr6:37630800-37631000	Enhancers	Colon Smooth Muscle	Colon
33	chr6:37630800-37631200	Enhancers	Fetal Muscle Leg	muscle
34	chr6:37630800-37631400	Enhancers	Fetal Lung	lung
35	chr6:37630800-37631800	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr6:37630800-37631800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:37630800-37631800	Enhancers	Fetal Stomach	stomach
38	chr6:37630800-37631800	Enhancers	NH-A	brain
39	chr6:37630800-37632600	Enhancers	HSMMtube	muscle
40	chr6:37630800-37633600	Enhancers	Brain Angular Gyrus	brain
41	chr6:37630800-37633600	Enhancers	Brain Hippocampus Middle	brain
42	chr6:37630800-37633800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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