Variant report

Variant	rs8009072
Chromosome Location	chr14:25159487-25159488
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10135076	0.82[EUR][1000 genomes]
rs10135223	0.85[EUR][1000 genomes]
rs10467736	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10467737	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12323930	0.85[EUR][1000 genomes]
rs12878578	0.82[CEU][hapmap]
rs17257110	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs1951590	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1957520	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2025213	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4982984	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4982986	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4982987	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7141222	0.85[EUR][1000 genomes]
rs72681039	0.85[EUR][1000 genomes]
rs9989226	0.85[EUR][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	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
3	nsv510631	chr14:25045183-25172311	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv901503	chr14:25133186-25172456	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8009072	CTSG	cis	multi-tissue	Pritchard
rs8009072	MDP1	cis	parietal	SCAN
rs8009072	PCK2	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:25151200-25160600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr14:25157400-25166800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
3	chr14:25157800-25159600	Weak transcription	Fetal Thymus	thymus
4	chr14:25157800-25159800	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr14:25157800-25159800	Weak transcription	GM12878-XiMat	blood
6	chr14:25157800-25162000	Weak transcription	Spleen	Spleen
7	chr14:25157800-25164000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr14:25158000-25164000	Weak transcription	Primary hematopoietic stem cells	blood
9	chr14:25158400-25159600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr14:25158400-25161800	Weak transcription	K562	blood
11	chr14:25158800-25159800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr14:25158800-25160200	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr14:25159000-25160200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr14:25159000-25160200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr14:25159200-25159800	Enhancers	Fetal Kidney	kidney
16	chr14:25159200-25160200	Enhancers	H1 Cell Line	embryonic stem cell
17	chr14:25159400-25159800	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr14:25159400-25160200	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr14:25159400-25166800	Enhancers	Primary T helper naive cells from peripheral blood	blood

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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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