Variant report

Variant	rs12156016
Chromosome Location	chr8:104918504-104918505
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10089467	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs10089978	0.97[ASN][1000 genomes]
rs10091544	0.89[ASN][1000 genomes]
rs10093057	0.86[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10103621	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs10108247	0.97[ASN][1000 genomes]
rs10505052	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10955332	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10955333	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10955334	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10955336	0.97[ASN][1000 genomes]
rs12155936	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12544699	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap]
rs12548406	0.86[EUR][1000 genomes]
rs12550348	0.89[EUR][1000 genomes]
rs12675494	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12679980	0.97[ASN][1000 genomes]
rs12682214	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1402442	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap]
rs1533733	0.84[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap]
rs1533734	1.00[CHB][hapmap];0.87[JPT][hapmap];0.86[YRI][hapmap]
rs16870788	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16870792	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16870816	0.98[ASN][1000 genomes]
rs17817357	0.97[ASN][1000 genomes]
rs2023025	0.84[EUR][1000 genomes]
rs2023026	0.85[EUR][1000 genomes]
rs2132644	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2173081	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2935296	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs3919234	0.94[ASN][1000 genomes]
rs4446700	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55880815	0.98[ASN][1000 genomes]
rs56232122	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56369021	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58139259	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58345884	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6986683	0.98[ASN][1000 genomes]
rs6986692	0.92[ASN][1000 genomes]
rs72681360	0.85[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs7357460	0.94[ASN][1000 genomes]
rs7836680	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[YRI][hapmap]
rs7840870	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9297340	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs9650010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9650011	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020476	chr8:104312212-104924482	Genic enhancers Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539704	chr8:104312212-104924482	Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	esv2752692	chr8:104520824-105123824	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1016387	chr8:104578389-104931853	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1031195	chr8:104601231-105194208	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
6	nsv831415	chr8:104907757-105115320	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12156016	RIMS2	cis	Thyroid	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104898200-104919000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:104899400-104933400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:104914800-104926000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr8:104918200-104922200	Weak transcription	Fetal Intestine Large	intestine
5	chr8:104918200-104922400	Weak transcription	Fetal Intestine Small	intestine
6	chr8:104918400-104919200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell

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