Variant report

Variant	rs11119881
Chromosome Location	chr1:212379741-212379742
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10779576	0.87[CHB][hapmap];0.81[JPT][hapmap];0.85[LWK][hapmap];0.87[MKK][hapmap];0.85[ASN][1000 genomes]
rs10863949	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10863950	0.85[EUR][1000 genomes]
rs1472225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1873298	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1962127	0.97[ASN][1000 genomes]
rs1967115	1.00[ASN][1000 genomes]
rs2358453	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2921128	0.82[CHB][hapmap]
rs4951578	1.00[ASN][1000 genomes]
rs4951584	0.87[CHB][hapmap]
rs6678627	0.91[ASN][1000 genomes]
rs7516619	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7548606	0.99[ASN][1000 genomes]
rs7549707	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs792433	0.82[CHB][hapmap]
rs792443	0.82[CHB][hapmap]
rs903123	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11119881	LOC148696	cis	parietal	SCAN
rs11119881	IL24	cis	cerebellum	SCAN
rs11119881	PPP2R5A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212368800-212391000	Weak transcription	Thymus	Thymus
2	chr1:212376000-212382400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr1:212376200-212380000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr1:212376200-212380600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:212376400-212380600	Weak transcription	Left Ventricle	heart
6	chr1:212376800-212382400	Weak transcription	HepG2	liver
7	chr1:212377600-212379800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:212378800-212380400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:212379000-212379800	Enhancers	K562	blood
10	chr1:212379200-212381600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr1:212379400-212380200	Enhancers	Skeletal Muscle Female	skeletal muscle
12	chr1:212379400-212381800	Enhancers	Adipose Nuclei	Adipose
13	chr1:212379600-212379800	Enhancers	Brain Anterior Caudate	brain
14	chr1:212379600-212382600	Weak transcription	Esophagus	oesophagus
15	chr1:212379600-212391600	Weak transcription	H1 Derived Neuronal Progenitor 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