Variant report

Variant	rs17661379
Chromosome Location	chr8:9221219-9221220
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-10A14.4.1-4	chr8:9220822-9221223	ucscGeneNc_uc003wsq_1

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10091555	0.81[EUR][1000 genomes]
rs10503385	0.85[EUR][1000 genomes]
rs11249915	0.81[EUR][1000 genomes]
rs12155604	0.88[EUR][1000 genomes]
rs12155605	0.88[EUR][1000 genomes]
rs12156035	0.88[EUR][1000 genomes]
rs17659866	0.81[EUR][1000 genomes]
rs17716678	0.81[EUR][1000 genomes]
rs28607267	0.88[EUR][1000 genomes]
rs61134018	0.95[AFR][1000 genomes]
rs6982301	0.81[EUR][1000 genomes]
rs6989012	0.81[EUR][1000 genomes]
rs6989928	0.81[EUR][1000 genomes]
rs6990709	0.81[EUR][1000 genomes]
rs6993236	0.81[EUR][1000 genomes]
rs6995025	0.98[AFR][1000 genomes]
rs7009542	0.81[EUR][1000 genomes]
rs73523012	0.98[AFR][1000 genomes]
rs73535350	0.89[AFR][1000 genomes]
rs73535357	0.98[AFR][1000 genomes]
rs9650631	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	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
3	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
4	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
5	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
6	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
7	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
8	nsv1030524	chr8:9183482-9412833	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv6073	chr8:9189800-9234741	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv890341	chr8:9192927-9243428	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv1031373	chr8:9216584-9234754	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv2764086	chr8:9216584-9334601	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17661379	MCPH1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9218400-9226400	Weak transcription	Liver	Liver
2	chr8:9221000-9221400	Enhancers	Brain Germinal Matrix	brain
3	chr8:9221200-9221600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr8:9221200-9221800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr8:9221200-9221800	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr8:9221200-9221800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr8:9221200-9221800	Enhancers	K562	blood

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