Variant report

Variant	rs11099841
Chromosome Location	chr4:152988490-152988491
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10006527	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11724208	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11737270	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11935999	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13130541	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13131963	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2059490	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2059493	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696129	0.82[EUR][1000 genomes]
rs4696313	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6535834	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6823781	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6852045	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7656585	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656970	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7681486	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695187	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7695682	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9996858	0.82[AMR][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	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv880341	chr4:152861685-153110256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv931416	chr4:152877808-153440553	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv461679	chr4:152935555-152992741	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv595734	chr4:152935555-152992741	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11099841	RNF175	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152983800-153000800	Enhancers	Fetal Thymus	thymus
2	chr4:152985200-152990000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr4:152985200-152993400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr4:152985200-152996200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr4:152985200-153000000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr4:152986200-152990000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr4:152986400-152989800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr4:152986600-152988600	Weak transcription	Psoas Muscle	Psoas
9	chr4:152986600-152989600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:152986600-152993200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:152986800-152998000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:152987200-152989400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr4:152987600-152989600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr4:152987600-152989600	Weak transcription	Primary T helper cells PMA-I stimulated	--
15	chr4:152987600-152990000	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr4:152988000-152989200	Weak transcription	Primary T cells from cord blood	blood
17	chr4:152988000-152989600	Weak transcription	Dnd41	blood
18	chr4:152988200-152989400	Weak transcription	Thymus	Thymus
19	chr4:152988400-152988800	Enhancers	Right Atrium	heart

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