Variant report

Variant	rs6573766
Chromosome Location	chr14:24852046-24852047
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Variant related genes	Relation type
ENSG00000100445	Chromatin interaction
ENSG00000139899	Chromatin interaction
ENSG00000100441	Chromatin interaction
ENSG00000100968	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 12 )

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

rs_ID	r²[population]
rs10131172	0.84[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11848279	0.80[ASW][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs1955915	0.91[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs57193392	0.83[ASN][1000 genomes]
rs7158837	0.88[TSI][hapmap]
rs8008583	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs9788516	0.84[CHB][hapmap];0.94[CHD][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.84[ASN][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	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6573766	TMEM55B	cis	cerebellum	SCAN
rs6573766	DHRS1	cis	cerebellum	SCAN
rs6573766	TEP1	cis	parietal	SCAN
rs6573766	CMA1	cis	cerebellum	SCAN
rs6573766	ADCY4	cis	multi-tissue	Pritchard
rs6573766	IRF9	cis	parietal	SCAN
rs6573766	NYNRIN	cis	cerebellum	SCAN
rs6573766	DAD1	cis	parietal	SCAN
rs6573766	NFATC4	cis	cerebellum	SCAN
rs6573766	GMPR2	cis	parietal	SCAN
rs6573766	OR11H6	cis	parietal	SCAN
rs6573766	ADCY4	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24842600-24852400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:24847000-24859600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr14:24847200-24857600	Weak transcription	Ovary	ovary
4	chr14:24847400-24857800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr14:24847600-24854600	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr14:24847800-24857400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr14:24848200-24852200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr14:24848200-24852600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr14:24848200-24857600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr14:24848200-24858400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr14:24848400-24856000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr14:24849400-24857400	Weak transcription	K562	blood
13	chr14:24850200-24854800	Weak transcription	Fetal Intestine Small	intestine
14	chr14:24850400-24855400	Weak transcription	Fetal Intestine Large	intestine
15	chr14:24851200-24857000	Weak transcription	Placenta	Placenta
16	chr14:24851400-24852200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr14:24851600-24853200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr14:24852000-24856000	Weak transcription	Fetal Kidney	kidney

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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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