Variant report

Variant	rs9462343
Chromosome Location	chr6:37620776-37620777
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:37483817..37486098-chr6:37619708..37622171,2	MCF-7	breast:
2	chr6:37601234..37603729-chr6:37618295..37621074,2	MCF-7	breast:
3	chr6:37615983..37618953-chr6:37619587..37621551,3	K562	blood:
4	chr6:37619715..37621661-chr6:37639970..37641510,2	K562	blood:
5	chr6:37617185..37618953-chr6:37619629..37621239,2	K562	blood:
6	chr6:37618578..37621552-chr6:37642899..37645409,2	K562	blood:
7	chr6:37614974..37617013-chr6:37618850..37621278,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000112139	Chromatin interaction

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

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

rs_ID	r²[population]
rs10807186	0.96[ASN][1000 genomes]
rs12195277	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs13198513	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13199974	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13203140	0.92[ASN][1000 genomes]
rs13204070	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13212859	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1738456	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1883899	0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1883900	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2273109	0.97[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2273110	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846873	0.97[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3846874	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3846876	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3846879	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3857567	0.88[ASN][1000 genomes]
rs3857568	0.96[ASN][1000 genomes]
rs3857571	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4236056	0.92[JPT][hapmap];0.96[ASN][1000 genomes]
rs4357132	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4711509	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6906090	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925749	0.90[CEU][hapmap];0.83[GIH][hapmap]
rs6930085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708020	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708021	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs708022	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7452633	0.96[ASN][1000 genomes]
rs7452676	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7452692	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs761413	0.83[ASN][1000 genomes]
rs7775837	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs804816	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804817	0.99[ASN][1000 genomes]
rs804830	0.81[JPT][hapmap]
rs804831	0.83[JPT][hapmap]
rs804859	0.83[JPT][hapmap]
rs813079	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9366945	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9369015	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9394447	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.94[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
rs9462343	MDGA1	cis	cerebellum	SCAN
rs9462343	GLP1R	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37599200-37621800	Weak transcription	NHLF	lung
2	chr6:37614200-37621800	Weak transcription	Aorta	Aorta
3	chr6:37617200-37621600	Weak transcription	Esophagus	oesophagus
4	chr6:37617200-37622400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:37618000-37621800	Weak transcription	Colon Smooth Muscle	Colon
6	chr6:37618200-37621800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:37618200-37631600	Weak transcription	Gastric	stomach
8	chr6:37618400-37622000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr6:37618800-37621800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr6:37618800-37622000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:37618800-37622000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:37619600-37621400	Enhancers	Brain Substantia Nigra	brain
13	chr6:37619800-37621200	Enhancers	Brain Cingulate Gyrus	brain
14	chr6:37619800-37621400	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr6:37620000-37622000	Weak transcription	Ovary	ovary
16	chr6:37620200-37621800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:37620200-37622400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:37620200-37632200	Weak transcription	Right Atrium	heart
19	chr6:37620400-37620800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr6:37620400-37621200	Enhancers	Brain Hippocampus Middle	brain
21	chr6:37620400-37622000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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