Variant report

Variant	rs4656945
Chromosome Location	chr1:160838107-160838108
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10908807	0.95[ASN][1000 genomes]
rs10908808	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11265498	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs11265499	0.81[ASN][1000 genomes]
rs11265500	0.95[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs11265501	0.96[ASN][1000 genomes]
rs11265504	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11265510	0.80[MEX][hapmap]
rs11578752	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12035295	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs12035537	0.81[ASN][1000 genomes]
rs12036607	1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs12036670	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12037395	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12037885	0.82[CHB][hapmap]
rs12038419	0.95[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12038600	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs12039896	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs12039959	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs12040152	0.95[CHB][hapmap]
rs12040750	0.96[ASN][1000 genomes]
rs12041508	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046019	0.81[ASN][1000 genomes]
rs12046021	0.81[ASN][1000 genomes]
rs12048113	0.91[CHB][hapmap]
rs12126310	0.88[LWK][hapmap];0.85[MEX][hapmap]
rs12409609	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12566557	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1333062	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1412849	0.95[ASN][1000 genomes]
rs17387157	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1855186	0.84[MEX][hapmap]
rs1855188	0.91[CHB][hapmap]
rs2039415	0.87[CEU][hapmap];0.90[MEX][hapmap]
rs2151293	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2184067	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2184068	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2184069	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2236515	0.92[CEU][hapmap];0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs2274905	0.92[CEU][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2274907	0.92[CEU][hapmap];0.84[GIH][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2274908	0.92[CEU][hapmap];0.84[GIH][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2274909	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2274910	0.88[ASW][hapmap];0.92[CEU][hapmap];0.84[GIH][hapmap];0.95[LWK][hapmap];0.95[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34067571	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs3766356	0.92[CEU][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3766357	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3766359	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3766378	0.91[CHB][hapmap]
rs3818724	0.86[AMR][1000 genomes]
rs3820094	0.92[CEU][hapmap];0.89[MEX][hapmap];0.82[EUR][1000 genomes]
rs3829790	0.80[MEX][hapmap]
rs4017448	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4017458	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4017459	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4017460	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656940	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs4656941	0.82[CHB][hapmap]
rs4656943	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs4656944	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656948	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4656949	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656950	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656951	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4656953	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4656955	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4656956	0.92[CEU][hapmap];0.90[MEX][hapmap];0.82[EUR][1000 genomes]
rs4656957	0.92[CEU][hapmap];0.90[MEX][hapmap];0.82[EUR][1000 genomes]
rs4656958	0.87[CEU][hapmap];0.90[MEX][hapmap]
rs4656971	0.80[MEX][hapmap]
rs58418513	0.81[ASN][1000 genomes]
rs61803285	0.81[ASN][1000 genomes]
rs6427550	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6427551	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6427552	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs6427553	0.86[AMR][1000 genomes]
rs6658416	0.86[AMR][1000 genomes]
rs6667400	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6676174	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6685693	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6698454	0.81[ASN][1000 genomes]
rs6699162	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6699166	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6700146	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6703406	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7410867	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs7411035	0.87[CEU][hapmap];0.83[LWK][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.86[AMR][1000 genomes]
rs7412693	0.85[CHB][hapmap]
rs7414728	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7419088	0.90[CHB][hapmap]
rs7419110	0.90[CHB][hapmap]
rs7419145	0.91[CHB][hapmap]
rs7524351	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7532133	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs869167	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs869168	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs914793	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs952804	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs955370	0.96[ASN][1000 genomes]
rs955371	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.82[MKK][hapmap];0.95[ASN][1000 genomes]
rs959047	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4656945	NDUFS2	cis	cerebellum	SCAN
rs4656945	SMG5	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160832600-160847400	Weak transcription	Spleen	Spleen
2	chr1:160833600-160840000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr1:160834600-160838400	Enhancers	Fetal Intestine Small	intestine
4	chr1:160834600-160849000	Weak transcription	Ovary	ovary
5	chr1:160835000-160838400	Enhancers	Fetal Intestine Large	intestine
6	chr1:160835400-160846400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:160836200-160844600	Weak transcription	A549	lung
8	chr1:160836400-160844600	Weak transcription	Pancreas	Pancrea
9	chr1:160836800-160839600	Enhancers	Monocytes-CD14+_RO01746	blood
10	chr1:160836800-160840000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:160837400-160840400	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr1:160837600-160839000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:160837600-160839400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr1:160837800-160838400	Enhancers	Primary B cells from cord blood	blood

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