Variant report

Variant	rs10100364
Chromosome Location	chr8:62253555-62253556
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10093364	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10094365	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10098539	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10098755	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs10098885	1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs10099169	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10111649	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs10111651	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.84[JPT][hapmap];0.91[ASN][1000 genomes]
rs10112069	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs10957192	1.00[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs12675558	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs12676622	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12679865	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1371741	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1371744	0.83[CHB][hapmap]
rs1486648	0.83[TSI][hapmap]
rs16927177	1.00[YRI][hapmap]
rs16927201	0.94[ASN][1000 genomes]
rs16927234	0.91[ASN][1000 genomes]
rs16927237	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs16927280	0.89[ASN][1000 genomes]
rs16927291	0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs16927299	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs17775880	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1822032	0.83[CHB][hapmap];0.84[CHD][hapmap]
rs1873888	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1992331	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1992332	1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1992333	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs2201261	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]
rs2220766	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap]
rs2610519	0.83[CHB][hapmap];0.90[CHD][hapmap]
rs28419747	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28477525	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28533992	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28886409	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3864676	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4147444	1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4147445	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs4147446	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs4395891	0.91[ASN][1000 genomes]
rs4737584	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4737585	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs4737586	0.86[ASN][1000 genomes]
rs4738885	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4738886	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4738887	0.86[ASN][1000 genomes]
rs4738888	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs4738889	0.87[ASN][1000 genomes]
rs56079904	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56161034	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59241236	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62524926	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6471947	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs6471949	0.92[ASN][1000 genomes]
rs6983659	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs6987161	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6994385	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6994804	0.93[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6998442	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7012230	1.00[CHB][hapmap];0.90[JPT][hapmap];0.93[ASN][1000 genomes]
rs72657057	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7386996	1.00[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs7820685	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs7836228	1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948922	chr8:61818964-62475097	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1024432	chr8:62086247-62898782	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv831336	chr8:62188396-62364873	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1027742	chr8:62206883-62613533	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv539633	chr8:62206883-62613533	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
6	nsv1021377	chr8:62214279-62596721	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv539634	chr8:62214279-62596721	ZNF genes & repeats Genic enhancers Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1029046	chr8:62224341-62535277	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10100364	CLVS1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:62249200-62253600	Weak transcription	Brain Angular Gyrus	brain
2	chr8:62251600-62263800	Weak transcription	Fetal Brain Female	brain
3	chr8:62252000-62255000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:62252600-62258000	Weak transcription	Fetal Brain Male	brain
5	chr8:62253000-62253600	Weak transcription	Brain Substantia Nigra	brain
6	chr8:62253200-62253600	Enhancers	Brain Hippocampus Middle	brain
7	chr8:62253400-62254000	Enhancers	Brain Germinal Matrix	brain
8	chr8:62253400-62254600	Enhancers	Cortex derived primary cultured neurospheres	brain

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