Variant report

Variant	rs10947686
Chromosome Location	chr6:37606805-37606806
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:37601453..37608472-chr6:37609186..37615415,9	K562	blood:

Variant related genes	Relation type
ENSG00000112139	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12191285	0.92[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12191311	0.82[TSI][hapmap]
rs4714087	0.80[EUR][1000 genomes]
rs708023	0.82[ASN][1000 genomes]
rs7748104	1.00[CEU][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7748388	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs804839	0.86[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10947686	MDGA1	cis	Skin Sun Exposed Lower leg	GTEx
rs10947686	MDGA1	cis	Esophagus Mucosa	GTEx
rs10947686	TBC1D22B	cis	cerebellum	SCAN
rs10947686	GLP1R	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:37594000-37615400	Weak transcription	Fetal Brain Female	brain
2	chr6:37599200-37615600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:37599200-37621800	Weak transcription	NHLF	lung
4	chr6:37600400-37611400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr6:37602200-37616600	Weak transcription	Right Atrium	heart
6	chr6:37602600-37610000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr6:37602800-37616400	Weak transcription	Ovary	ovary
8	chr6:37604000-37610000	Weak transcription	Fetal Brain Male	brain
9	chr6:37604000-37611800	Weak transcription	Brain Germinal Matrix	brain
10	chr6:37604200-37614600	Strong transcription	Fetal Stomach	stomach
11	chr6:37604400-37611600	Weak transcription	Small Intestine	intestine
12	chr6:37605000-37611600	Weak transcription	Gastric	stomach
13	chr6:37605400-37607600	Enhancers	Hela-S3	cervix
14	chr6:37605400-37609000	Weak transcription	Spleen	Spleen
15	chr6:37605600-37607400	Enhancers	HMEC	breast
16	chr6:37605600-37607400	Enhancers	K562	blood
17	chr6:37605800-37607200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr6:37605800-37607200	Enhancers	A549	lung
19	chr6:37606200-37607000	Flanking Active TSS	NHEK	skin
20	chr6:37606200-37607400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:37606200-37609200	Enhancers	Esophagus	oesophagus
22	chr6:37606400-37607000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:37606400-37607000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr6:37606400-37607000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr6:37606400-37607000	Enhancers	Adipose Nuclei	Adipose
26	chr6:37606400-37607000	Enhancers	HSMMtube	muscle
27	chr6:37606400-37607200	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr6:37606600-37607000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
29	chr6:37606600-37607200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:37606600-37607400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:37606800-37607000	Bivalent Enhancer	Stomach Mucosa	stomach
32	chr6:37606800-37607000	Bivalent Enhancer	HepG2	liver
33	chr6:37606800-37607400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr6:37606800-37611800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr6:37606800-37615600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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