Variant report

Variant	rs2525549
Chromosome Location	chr7:99533111-99533112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 9 )

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

rs_ID	r²[population]
rs1981549	0.97[ASN][1000 genomes]
rs2040787	0.97[ASN][1000 genomes]
rs2404975	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525535	0.97[ASN][1000 genomes]
rs2525536	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525539	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.97[ASN][1000 genomes]
rs2525540	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525543	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2525545	0.95[ASN][1000 genomes]
rs2525550	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2525558	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2527887	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2527888	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2527889	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2527898	0.98[ASN][1000 genomes]
rs35656988	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829865	chr7:99430678-99755141	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1131 gene(s)	inside rSNPs	diseases
2	esv1830649	chr7:99430678-99755141	Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' 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	1131 gene(s)	inside rSNPs	diseases
3	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
4	nsv607930	chr7:99525241-99602191	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
5	esv1828362	chr7:99530233-99628773	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2525549	TECPR1	cis	cerebellum	SCAN
rs2525549	NAPEPLD	cis	parietal	SCAN
rs2525549	TRIM4	Cis_1M	lymphoblastoid	RTeQTL
rs2525549	OR2AE1	cis	parietal	SCAN
rs2525549	TRIM4	cis	Thyroid	GTEx
rs2525549	BUD31	cis	parietal	SCAN
rs2525549	TRIM4	cis	multi-tissue	Pritchard
rs2525549	ZSCAN21	cis	parietal	SCAN
rs2525549	GATS	cis	parietal	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99528000-99535600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr7:99532000-99535600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr7:99532200-99533400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr7:99532200-99533400	Enhancers	K562	blood
5	chr7:99532400-99533400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr7:99532400-99533400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:99532400-99548000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr7:99532600-99533200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr7:99532600-99533200	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr7:99532600-99533400	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr7:99532600-99533400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
12	chr7:99533000-99533200	Strong transcription	H9 Cell Line	embryonic stem cell
13	chr7:99533000-99533200	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr7:99533000-99533400	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

Quick Search:

Input of quick search could be:

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

what's new

Quick links