Variant report

Variant	rs11257854
Chromosome Location	chr10:6329997-6329998
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10906207	0.84[ASN][1000 genomes]
rs12259346	0.86[ASN][1000 genomes]
rs4403713	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4420170	0.83[CHD][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs4747994	0.84[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6602609	0.82[ASN][1000 genomes]
rs7088356	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7896262	0.87[ASN][1000 genomes]
rs7906792	0.84[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7918684	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7921642	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1054044	chr10:6155144-6487217	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1041039	chr10:6217724-6354858	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv894836	chr10:6246678-6435374	Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv430123	chr10:6309402-6448384	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
6	nsv430125	chr10:6322167-6477267	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11257854	IL2RA	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6317800-6332600	Weak transcription	Thymus	Thymus
2	chr10:6318000-6337600	Weak transcription	Primary B cells from cord blood	blood
3	chr10:6318200-6333000	Weak transcription	Primary T cells from cord blood	blood
4	chr10:6318200-6333200	Weak transcription	Adipose Nuclei	Adipose
5	chr10:6318200-6337800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr10:6322200-6330000	Weak transcription	Aorta	Aorta
7	chr10:6322600-6337600	Weak transcription	Spleen	Spleen
8	chr10:6322600-6339000	Weak transcription	Esophagus	oesophagus
9	chr10:6322800-6332400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr10:6323600-6332600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr10:6326000-6332800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr10:6329200-6332600	Weak transcription	Gastric	stomach
13	chr10:6329400-6332600	Weak transcription	Stomach Mucosa	stomach
14	chr10:6329600-6332600	Weak transcription	Fetal Intestine Small	intestine
15	chr10:6329600-6332800	Weak transcription	HepG2	liver
16	chr10:6329800-6332600	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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