Variant report

Variant	rs11099840
Chromosome Location	chr4:152947169-152947170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10003555	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12509941	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13106080	1.00[ASN][1000 genomes]
rs13107216	1.00[CHB][hapmap]
rs13123917	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13130547	1.00[ASN][1000 genomes]
rs13130730	1.00[ASN][1000 genomes]
rs13143024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13149643	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1469241	1.00[ASN][1000 genomes]
rs17276149	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17276212	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4549360	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4696123	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7683987	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7695495	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs890177	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs919013	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9997649	0.91[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	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

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152944000-152947400	Enhancers	Fetal Thymus	thymus
2	chr4:152944800-152947400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
3	chr4:152945000-152949400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:152945200-152947200	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr4:152945400-152947600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr4:152945800-152950800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr4:152946200-152947400	Enhancers	Dnd41	blood
8	chr4:152946400-152949400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:152946600-152947200	Enhancers	Thymus	Thymus

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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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