Variant report

Variant	rs11935999
Chromosome Location	chr4:153004152-153004153
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10006527	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11099841	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11724208	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11737270	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13130541	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13131963	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2059490	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2059493	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4696129	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4696313	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6535834	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6823781	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6852045	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7656585	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7656970	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7681486	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7695187	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7695682	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11935999	RP11-18H21.1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152997400-153011800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:153001200-153008800	Enhancers	Thymus	Thymus
3	chr4:153002600-153010400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr4:153002800-153006000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr4:153003000-153006000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr4:153003200-153006000	Weak transcription	Primary T cells from cord blood	blood
7	chr4:153003200-153007200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr4:153003200-153009600	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr4:153003200-153013800	Enhancers	Fetal Thymus	thymus
10	chr4:153003600-153006200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr4:153003600-153009600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr4:153003600-153014000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr4:153003800-153006200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr4:153004000-153006200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr4:153004000-153006400	Weak transcription	Dnd41	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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