Variant report

Variant	rs12664474
Chromosome Location	chr6:25876089-25876090
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10498731	0.95[JPT][hapmap]
rs1892247	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2328896	0.83[ASN][1000 genomes]
rs3799367	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs4573076	0.81[ASN][1000 genomes]
rs56069761	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58011016	0.88[ASN][1000 genomes]
rs9358890	0.95[JPT][hapmap]
rs9379800	0.90[AMR][1000 genomes];0.83[EUR][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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv427747	chr6:25641380-25908218	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1030351	chr6:25813178-26352046	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1189 gene(s)	inside rSNPs	diseases
5	nsv1023453	chr6:25853830-26528250	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1201 gene(s)	inside rSNPs	diseases
6	nsv1025237	chr6:25874326-26280867	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases
7	nsv538163	chr6:25874326-26280867	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1166 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12664474	HIST1H2BC	cis	cerebellum	SCAN
rs12664474	HIST1H3F	cis	cerebellum	SCAN
rs12664474	HIST1H2BI	cis	cerebellum	SCAN
rs12664474	GPX6	cis	parietal	SCAN
rs12664474	TDP2	cis	parietal	SCAN
rs12664474	HIST1H4L	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:25873000-25876400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr6:25873000-25877000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr6:25873000-25877000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:25873800-25876400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:25874200-25877400	Enhancers	HepG2	liver
6	chr6:25874800-25877200	Enhancers	Liver	Liver
7	chr6:25875400-25882200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr6:25875600-25876800	Weak transcription	Ovary	ovary
9	chr6:25875600-25877400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr6:25875800-25876200	Weak transcription	A549	lung

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

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