Variant report

Variant	rs9407897
Chromosome Location	chr9:18359014-18359015
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10511652	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10756959	0.91[ASN][1000 genomes]
rs10810958	0.99[ASN][1000 genomes]
rs12338293	0.87[ASN][1000 genomes]
rs12341057	0.88[ASN][1000 genomes]
rs12350298	0.88[ASN][1000 genomes]
rs1340044	0.91[ASN][1000 genomes]
rs2791442	0.96[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4961642	0.88[ASN][1000 genomes]
rs7020284	0.91[CHB][hapmap];0.83[CHD][hapmap];0.86[ASN][1000 genomes]
rs7024252	0.91[CHB][hapmap];0.86[ASN][1000 genomes]
rs7028032	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7031026	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7047314	0.91[ASN][1000 genomes]
rs7859508	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7861774	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9406744	0.84[CEU][hapmap]
rs9406745	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831522	chr9:18231982-18459492	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2764161	chr9:18247433-18443060	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv892684	chr9:18261485-18401585	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv892687	chr9:18303691-18430297	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv525743	chr9:18312578-18359014	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv1831194	chr9:18355044-18369216	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9407897	MLLT3	cis	parietal	SCAN
rs9407897	CDKN2B	cis	cerebellum	SCAN
rs9407897	IFNW1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18333400-18368200	Weak transcription	Aorta	Aorta
2	chr9:18346600-18362000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr9:18347600-18360400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr9:18351800-18361600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr9:18356400-18363200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr9:18357400-18364200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr9:18358000-18364200	Enhancers	NHDF-Ad	bronchial
8	chr9:18358000-18364400	Enhancers	Osteobl	bone
9	chr9:18358400-18360800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr9:18358600-18359200	Enhancers	NH-A	brain
11	chr9:18358600-18360200	Flanking Active TSS	HUVEC	blood vessel
12	chr9:18358600-18360600	Enhancers	HSMM	muscle
13	chr9:18358600-18361000	Enhancers	Muscle Satellite Cultured Cells	--
14	chr9:18358800-18360400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr9:18358800-18360600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:18358800-18362600	Weak transcription	Primary B cells from cord blood	blood
17	chr9:18359000-18359200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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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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