Variant report

Variant	rs11207196
Chromosome Location	chr1:58790501-58790502
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 7 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1213636	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1213642	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72669807	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1015057	chr1:57976993-58793962	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv431379	chr1:58224212-58802608	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1008968	chr1:58582159-58982440	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv534974	chr1:58582159-58982440	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11207196	USP24	cis	parietal	SCAN
rs11207196	PRKAA2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:58787400-58791600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr1:58787600-58791600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:58789000-58793000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
4	chr1:58789600-58791000	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr1:58789600-58791200	Flanking Active TSS	Primary T cells from cord blood	blood
6	chr1:58789800-58790800	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr1:58789800-58790800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr1:58789800-58791000	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr1:58789800-58791000	Enhancers	Thymus	Thymus
10	chr1:58789800-58791800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr1:58789800-58792200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr1:58790000-58790800	Enhancers	Dnd41	blood
13	chr1:58790200-58790600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr1:58790200-58790800	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr1:58790200-58790800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:58790400-58790800	Enhancers	Fetal Thymus	thymus
17	chr1:58790400-58791000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr1:58790400-58792000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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