Variant report

Variant	rs3846879
Chromosome Location	chr6:37628197-37628198
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:37623883..37625682-chr6:37627953..37629505,2	K562	blood:
2	chr6:37625457..37629220-chr6:37629233..37634339,4	K562	blood:

Variant related genes	Relation type
ENSG00000112139	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10807186	0.98[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];1.00[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	0.93[ASN][1000 genomes]
rs13203140	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13204070	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13212859	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[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	0.95[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1883900	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]
rs2273109	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2273110	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3846873	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3846874	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3846876	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3857567	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3857568	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3857570	0.95[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];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4236056	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.97[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];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4711509	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[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	0.98[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];0.83[AFR][1000 genomes];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];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs761413	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7775837	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[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	0.81[JPT][hapmap]
rs804831	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs804859	0.87[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];0.93[ASN][1000 genomes]
rs9462343	0.93[CHB][hapmap];1.00[CHD][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3846879	MDGA1	cis	Esophagus Mucosa	GTEx
rs3846879	MDGA1	cis	Skin Sun Exposed Lower leg	GTEx
rs3846879	MDGA1	cis	cerebellum	SCAN

Chromatin state (count:29 , 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	chr6:37621400-37630800	Weak transcription	Brain Angular Gyrus	brain
4	chr6:37621400-37630800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:37621600-37631400	Weak transcription	Fetal Brain Male	brain
6	chr6:37622200-37630800	Weak transcription	Brain Hippocampus Middle	brain
7	chr6:37622200-37630800	Weak transcription	Colon Smooth Muscle	Colon
8	chr6:37622400-37632400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:37622400-37633000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr6:37622600-37630600	Weak transcription	NHLF	lung
11	chr6:37623400-37628800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr6:37624000-37628800	Weak transcription	Colonic Mucosa	Colon
13	chr6:37625600-37628600	Weak transcription	NHDF-Ad	bronchial
14	chr6:37625600-37630600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr6:37625800-37629000	Weak transcription	Aorta	Aorta
16	chr6:37626000-37628800	Weak transcription	Ovary	ovary
17	chr6:37626000-37630800	Weak transcription	NH-A	brain
18	chr6:37626000-37633400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr6:37626000-37635000	Weak transcription	A549	lung
20	chr6:37626200-37629400	Weak transcription	Brain Germinal Matrix	brain
21	chr6:37626400-37631400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr6:37626600-37628200	ZNF genes & repeats	Fetal Stomach	stomach
23	chr6:37626600-37631000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:37627000-37631200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr6:37627600-37628200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:37627600-37628600	ZNF genes & repeats	Fetal Brain Female	brain
27	chr6:37627600-37629400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr6:37628000-37628400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr6:37628000-37628800	Weak transcription	Pancreas	Pancrea

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