Variant report

Variant	rs978825
Chromosome Location	chr8:104853667-104853668
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:104852211..104853787-chr8:104853794..104855362,2	MCF-7	breast:

Extended variants
information (count: 114 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10808385	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10955327	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10955328	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12541956	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12542880	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12543866	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12543980	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12544699	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12544763	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12545944	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12546381	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12546553	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12547180	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12547819	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12548029	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12548032	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12548742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12548865	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12675210	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12675778	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12676673	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12680651	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12680654	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1402442	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1496846	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1521057	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1521059	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1521060	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1521061	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1533733	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1533734	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1593497	0.97[ASN][1000 genomes]
rs1607912	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16870589	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16870611	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16870632	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs16870636	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16870649	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16870656	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16870702	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16870707	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16870714	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16870727	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16870730	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16870733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16870735	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16870769	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16870772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16870774	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16870776	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16870786	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16870788	0.88[ASN][1000 genomes]
rs1851151	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1874519	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2023027	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2067550	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2080611	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2111494	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2388783	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2388849	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28362512	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28362513	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34195802	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34738173	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35470583	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3824118	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4301418	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4333556	0.97[ASN][1000 genomes]
rs4532569	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4541867	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4549736	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56101019	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56139465	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56990053	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs57397838	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57643265	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs57901487	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58631312	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58858789	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59382988	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59732166	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60253339	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61099915	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61137924	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61300996	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61556831	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61618724	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6468894	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6987829	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6990561	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6991464	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6991576	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6997813	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7009840	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7461785	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7462974	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7463540	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7818306	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7826803	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7832196	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7833762	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7836355	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7836680	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9650010	0.83[CEU][hapmap]

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	nsv429931	chr8:104097396-104878014	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv1023048	chr8:104355188-104872701	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh 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	39 gene(s)	inside rSNPs	diseases
5	nsv539705	chr8:104355188-104872701	ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1021345	chr8:104361854-104879684	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv1032085	chr8:104362187-104878345	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs978825	RIMS2	cis	Thyroid	GTEx
rs978825	RP11-1C8.7	cis	Thyroid	GTEx
rs978825	PABPC1	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:104805800-104858600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:104853400-104853800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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