Variant report

Variant	rs12203410
Chromosome Location	chr6:30978746-30978747
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs12198448	0.89[ASN][1000 genomes]
rs12204688	0.87[ASN][1000 genomes]
rs12204735	0.89[ASN][1000 genomes]
rs12204842	0.89[ASN][1000 genomes]
rs12207166	0.89[ASN][1000 genomes]
rs12207266	0.85[ASN][1000 genomes]
rs12208652	0.89[ASN][1000 genomes]
rs12211072	0.89[ASN][1000 genomes]
rs12215548	0.89[ASN][1000 genomes]
rs17196346	0.89[ASN][1000 genomes]
rs28360975	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3869095	0.89[ASN][1000 genomes]
rs3873342	0.85[ASN][1000 genomes]
rs41288689	0.85[ASN][1000 genomes]
rs57426248	0.89[ASN][1000 genomes]
rs6909998	0.89[ASN][1000 genomes]
rs6910464	0.87[ASN][1000 genomes]
rs6910475	0.89[ASN][1000 genomes]
rs6926507	0.81[ASN][1000 genomes]
rs73727153	0.89[ASN][1000 genomes]
rs73727154	0.89[ASN][1000 genomes]
rs73727156	0.89[ASN][1000 genomes]
rs73727158	0.89[ASN][1000 genomes]
rs73727160	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	esv3358044	chr6:30940552-31000175	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1023108	chr6:30944982-30990490	Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv462745	chr6:30955681-30987176	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv601485	chr6:30955681-30987176	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv601486	chr6:30957618-30980015	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv970676	chr6:30966672-30987268	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv601487	chr6:30972589-30991559	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12203410	ZNF192	cis	cerebellum	SCAN
rs12203410	HMGA1	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30972600-30997600	Weak transcription	Right Atrium	heart
2	chr6:30975000-30979400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:30977800-30978800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:30978000-30979000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:30978200-30978800	Enhancers	HMEC	breast
6	chr6:30978200-30979000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:30978200-30979200	Enhancers	Osteobl	bone
8	chr6:30978400-30978800	Enhancers	HSMM	muscle
9	chr6:30978400-30978800	Enhancers	NH-A	brain
10	chr6:30978400-30979200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr6:30978600-30980000	Enhancers	HepG2	liver

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