Variant report

Variant	rs12212125
Chromosome Location	chr6:119946363-119946364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1572956	0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2064570	0.81[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2066283	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9372543	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9398518	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9401159	0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3447598	chr6:119558591-120119384	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	esv3389526	chr6:119558598-120190087	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1027904	chr6:119709488-120001986	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv533518	chr6:119712186-119998618	ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv3442553	chr6:119742069-120076777	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1027370	chr6:119869409-120056608	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv538431	chr6:119869409-120056608	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12212125	GPRC6A	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119930600-119948000	Weak transcription	Primary hematopoietic stem cells	blood
2	chr6:119940400-119949800	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr6:119943200-119948400	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr6:119943200-119948600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr6:119943400-119948200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr6:119943400-119948400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr6:119943600-119948000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:119943600-119948600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:119943800-119948800	Weak transcription	NHDF-Ad	bronchial
10	chr6:119944000-119948200	Weak transcription	HMEC	breast
11	chr6:119944000-119948400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr6:119944000-119949000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr6:119944200-119948800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:119945000-119949200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr6:119945200-119948800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:119945400-119948800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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