Variant report

Variant	rs4656953
Chromosome Location	chr1:160845842-160845843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10908808	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908809	0.81[EUR][1000 genomes]
rs11265504	0.84[EUR][1000 genomes]
rs11265510	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11265514	0.80[AFR][1000 genomes]
rs11578752	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11587040	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs12041508	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12126310	0.87[YRI][hapmap]
rs12409609	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12566557	0.82[EUR][1000 genomes]
rs1333062	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17387157	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1855186	0.83[CEU][hapmap]
rs1855187	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2039415	0.96[CEU][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs2151293	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2184067	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2184068	0.84[EUR][1000 genomes]
rs2184069	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2236515	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2274905	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2274907	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2274908	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2274909	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2274910	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2297559	0.91[EUR][1000 genomes]
rs34067571	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766356	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766357	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3766359	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3818724	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3820094	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4017448	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4017458	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4017459	0.83[EUR][1000 genomes]
rs4017460	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4656944	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4656945	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4656948	0.80[EUR][1000 genomes]
rs4656949	0.84[EUR][1000 genomes]
rs4656950	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4656951	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4656955	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656956	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4656957	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4656958	0.96[CEU][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs4656959	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6427550	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6427551	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6427552	1.00[CEU][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6427553	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6658416	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6667400	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6671490	0.91[EUR][1000 genomes]
rs6676174	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6685693	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6694415	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6699162	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6699166	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6700146	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6703406	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6704490	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7411035	0.96[CEU][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7414728	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7414826	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7516660	0.84[CEU][hapmap];0.83[JPT][hapmap]
rs7524351	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7532133	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7551697	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs869167	0.84[EUR][1000 genomes]
rs869168	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs914793	0.83[EUR][1000 genomes]
rs952804	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs959047	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv464161	chr1:160747615-160852046	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS 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	10 gene(s)	inside rSNPs	diseases
2	nsv548057	chr1:160747615-160852046	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4656953	RP11-312J18.6	cis	Thyroid	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160832600-160847400	Weak transcription	Spleen	Spleen
2	chr1:160834600-160849000	Weak transcription	Ovary	ovary
3	chr1:160835400-160846400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:160839400-160846000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:160840800-160846600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:160844000-160846800	Enhancers	Fetal Intestine Small	intestine
7	chr1:160844400-160847600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:160844600-160846800	Enhancers	Fetal Intestine Large	intestine
9	chr1:160845400-160847200	Enhancers	Primary neutrophils fromperipheralblood	blood
10	chr1:160845600-160846000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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