Variant report

Variant	rs2420514
Chromosome Location	chr1:169877058-169877059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169866713..169870686-chr1:169874035..169877977,4	K562	blood:
2	chr1:169875733..169878335-chr1:170499104..170501946,2	MCF-7	breast:
3	chr1:169867701..169870686-chr1:169875443..169877977,2	K562	blood:

Variant related genes	Relation type
ENSG00000231407	Chromatin interaction
ENSG00000120370	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10733054	0.96[CEU][hapmap]
rs10737549	0.95[CEU][hapmap];0.89[EUR][1000 genomes]
rs10800479	0.92[EUR][1000 genomes]
rs10800480	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10800481	0.92[EUR][1000 genomes]
rs10800483	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10800485	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10800486	0.96[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10919239	0.95[CEU][hapmap]
rs10919245	0.92[EUR][1000 genomes]
rs10919248	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10919251	0.92[EUR][1000 genomes]
rs10919263	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12023275	0.80[CHB][hapmap]
rs12133843	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs12563479	0.80[CHB][hapmap]
rs12724797	0.83[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs1883436	0.91[EUR][1000 genomes]
rs1883437	0.87[AMR][1000 genomes]
rs2056980	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2056981	0.96[CEU][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs2152831	0.80[CHB][hapmap]
rs2179396	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs2281039	0.92[EUR][1000 genomes]
rs2294322	0.92[EUR][1000 genomes]
rs2420512	0.92[EUR][1000 genomes]
rs2485462	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2491087	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2491088	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2750016	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2750020	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2806382	0.82[EUR][1000 genomes]
rs2806386	0.92[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2806388	0.84[EUR][1000 genomes]
rs2806393	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2901179	1.00[YRI][hapmap]
rs3753308	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3766132	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs3766134	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs3766137	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs3766142	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3766148	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs3766151	0.96[CEU][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3766154	0.96[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3766155	0.83[CHB][hapmap];0.96[JPT][hapmap];0.86[ASN][1000 genomes]
rs4141917	0.84[CEU][hapmap];0.80[CHB][hapmap]
rs4376791	0.90[EUR][1000 genomes]
rs4508080	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs4614317	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4615900	0.96[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs4656196	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4656721	1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs4656725	0.89[EUR][1000 genomes]
rs6427220	0.88[CEU][hapmap]
rs6427225	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs6427228	0.87[EUR][1000 genomes]
rs6656965	0.93[EUR][1000 genomes]
rs6669794	0.89[EUR][1000 genomes]
rs6670818	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6671752	0.85[EUR][1000 genomes]
rs6673712	0.80[CHB][hapmap]
rs6680508	0.92[CEU][hapmap]
rs6680650	0.92[EUR][1000 genomes]
rs6682137	0.88[EUR][1000 genomes]
rs6682835	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6683056	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6702969	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs717481	0.93[EUR][1000 genomes]
rs732185	0.92[CEU][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7517490	0.82[CHB][hapmap]
rs7525259	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs7530237	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs7545011	0.92[EUR][1000 genomes]
rs9287097	0.96[CEU][hapmap];0.91[EUR][1000 genomes]

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	esv3451367	chr1:169630075-169976964	Strong transcription Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	esv1814601	chr1:169782006-169885186	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	esv1821503	chr1:169782006-169885186	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1847722	chr1:169782006-169885186	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	esv2757760	chr1:169782006-169885186	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	esv2758976	chr1:169782006-169885186	Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv428268	chr1:169782006-169885186	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	esv1845220	chr1:169782006-169933886	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2420514	SCYL3	Cis_1M	lymphoblastoid	RTeQTL
rs2420514	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169872800-169877600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:169872800-169878000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:169872800-169887800	Weak transcription	Primary T cells from cord blood	blood
4	chr1:169873200-169877400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:169873200-169877600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:169873200-169877600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr1:169873200-169877600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr1:169873400-169877600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:169875800-169889800	Weak transcription	Fetal Brain Female	brain
10	chr1:169876200-169903600	Weak transcription	Aorta	Aorta
11	chr1:169876600-169877800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:169876600-169883000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:169876800-169877400	ZNF genes & repeats	GM12878-XiMat	blood
14	chr1:169876800-169883400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:169877000-169884000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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