Variant report

Variant	rs3741085
Chromosome Location	chr11:57166969-57166970
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1049272	0.84[EUR][1000 genomes]
rs1049273	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10792093	0.82[EUR][1000 genomes]
rs10792094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10896614	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10896615	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11228987	0.82[YRI][hapmap]
rs11229005	1.00[MKK][hapmap]
rs11229017	0.84[AFR][1000 genomes]
rs11606592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4938863	0.85[CEU][hapmap]
rs7106575	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers 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 miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3741085	OR10V1	cis	parietal	SCAN
rs3741085	TIMM10	cis	parietal	SCAN
rs3741085	OR4A15	cis	cerebellum	SCAN
rs3741085	MS4A7	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57149200-57171000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr11:57151000-57170200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr11:57164200-57172600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr11:57164400-57167000	Enhancers	K562	blood
5	chr11:57165000-57167400	Weak transcription	Liver	Liver
6	chr11:57165000-57174000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:57165200-57172800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr11:57165400-57173400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr11:57165800-57171200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:57166200-57167800	Enhancers	NHEK	skin
11	chr11:57166400-57167200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr11:57166400-57167400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr11:57166400-57167400	Enhancers	HMEC	breast
14	chr11:57166600-57167400	Enhancers	HUVEC	blood vessel
15	chr11:57166600-57167600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr11:57166600-57169000	Enhancers	HepG2	liver
17	chr11:57166800-57169200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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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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