Variant report

Variant	rs852931
Chromosome Location	chr6:72178627-72178628
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10155718	0.82[ASN][1000 genomes]
rs1738070	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1738072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4141421	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs503993	0.81[EUR][1000 genomes]
rs504983	0.81[EUR][1000 genomes]
rs701698	0.97[ASN][1000 genomes]
rs701699	0.97[ASN][1000 genomes]
rs852919	0.82[ASN][1000 genomes]
rs852920	0.82[ASN][1000 genomes]
rs852922	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs852923	0.82[ASN][1000 genomes]
rs852925	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs852927	0.82[ASN][1000 genomes]
rs852928	0.97[ASN][1000 genomes]
rs852929	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852930	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852961	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs852966	0.85[CHD][hapmap];0.83[JPT][hapmap]
rs852971	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830684	chr6:72094842-72282684	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	488 gene(s)	inside rSNPs	diseases
2	nsv1025409	chr6:72175998-72205044	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs852931	LMBRD1	cis	cerebellum	SCAN
rs852931	BAI3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:72176600-72178800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr6:72177600-72178800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr6:72177800-72179400	Enhancers	Fetal Lung	lung
4	chr6:72177800-72179800	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr6:72178000-72178800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr6:72178000-72179800	Enhancers	NHLF	lung
7	chr6:72178200-72179200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:72178200-72179200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr6:72178200-72179400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:72178200-72179400	Flanking Active TSS	NH-A	brain
11	chr6:72178200-72179400	Flanking Active TSS	Osteobl	bone
12	chr6:72178200-72179600	Enhancers	Fetal Kidney	kidney
13	chr6:72178200-72179600	Enhancers	HMEC	breast
14	chr6:72178200-72179800	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr6:72178400-72178800	Enhancers	Brain Anterior Caudate	brain
16	chr6:72178400-72178800	Active TSS	HSMM	muscle
17	chr6:72178400-72179000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr6:72178400-72179200	Active TSS	HSMMtube	muscle
19	chr6:72178400-72179400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:72178400-72179400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:72178400-72179400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr6:72178400-72179400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr6:72178600-72178800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr6:72178600-72178800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:72178600-72178800	Active TSS	Aorta	Aorta
26	chr6:72178600-72178800	Enhancers	Brain Germinal Matrix	brain
27	chr6:72178600-72178800	Active TSS	Stomach Smooth Muscle	stomach
28	chr6:72178600-72179000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr6:72178600-72179000	Active TSS	NHDF-Ad	bronchial
30	chr6:72178600-72179200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr6:72178600-72179200	Enhancers	Adipose Nuclei	Adipose
32	chr6:72178600-72179400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr6:72178600-72179400	Enhancers	NHEK	skin
34	chr6:72178600-72179600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr6:72178600-72187800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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