Variant report

Variant	rs17659159
Chromosome Location	chr8:9175012-9175013
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:9173249..9175373-chr8:9182159..9185113,2	MCF-7	breast:
2	chr8:9173793..9177348-chr8:9178573..9182630,4	K562	blood:

Variant related genes	Relation type
ENSG00000254235	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10091555	0.93[EUR][1000 genomes]
rs10503385	0.88[CEU][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11249915	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12155604	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12155605	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12156035	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13439171	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13439686	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17659068	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17659866	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17660164	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17660611	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17716095	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17716678	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2054346	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2054347	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2054348	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28607267	0.85[EUR][1000 genomes]
rs3932954	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6982301	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6989012	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6989928	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6990709	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6993236	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6994507	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7009542	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs922269	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9650631	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917117	chr8:8621658-9313799	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1022468	chr8:8857853-9209167	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv539460	chr8:8857853-9209167	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv817373	chr8:8857854-9361049	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv949434	chr8:8993551-9318404	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1018847	chr8:9017110-9216354	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1022967	chr8:9023771-9261351	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	nsv539462	chr8:9023771-9261351	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
10	nsv497927	chr8:9097611-9544519	Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17659159	MCPH1	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9170000-9175200	Weak transcription	Left Ventricle	heart
2	chr8:9171400-9176200	Weak transcription	Right Ventricle	heart
3	chr8:9174200-9175400	Enhancers	Psoas Muscle	Psoas
4	chr8:9174200-9177800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr8:9174400-9176400	Enhancers	Ovary	ovary
6	chr8:9174600-9175400	Enhancers	Fetal Heart	heart
7	chr8:9174600-9175600	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr8:9174600-9176600	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr8:9174600-9177200	Enhancers	Right Atrium	heart
10	chr8:9174600-9178400	Enhancers	Brain Cingulate Gyrus	brain
11	chr8:9174600-9178800	Enhancers	Brain Substantia Nigra	brain
12	chr8:9174800-9176000	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr8:9174800-9176400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr8:9174800-9176400	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr8:9174800-9177000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr8:9174800-9177200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr8:9174800-9178000	Enhancers	Adipose Nuclei	Adipose
18	chr8:9174800-9178600	Enhancers	Brain Hippocampus Middle	brain
19	chr8:9175000-9175400	Flanking Active TSS	Liver	Liver
20	chr8:9175000-9175600	Weak transcription	Osteobl	bone
21	chr8:9175000-9176200	Weak transcription	Brain Inferior Temporal Lobe	brain

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