Variant report

Variant	rs2056980
Chromosome Location	chr1:169883039-169883040
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169863487..169865405-chr1:169882715..169884373,2	K562	blood:
2	chr1:169881052..169883977-chr1:169885843..169888269,2	MCF-7	breast:
3	chr1:169861017..169866202-chr1:169878725..169885490,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10733054	0.88[CEU][hapmap]
rs10737549	0.91[CEU][hapmap];0.81[TSI][hapmap]
rs10800479	0.82[EUR][1000 genomes]
rs10800480	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10800481	0.82[EUR][1000 genomes]
rs10800483	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10800485	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs10800486	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs10919239	0.87[CEU][hapmap]
rs10919245	0.82[EUR][1000 genomes]
rs10919248	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs10919251	0.82[EUR][1000 genomes]
rs10919263	0.81[EUR][1000 genomes]
rs12133843	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs12724797	0.81[MEX][hapmap]
rs16862831	0.85[YRI][hapmap]
rs1883436	0.80[EUR][1000 genomes]
rs2056981	0.88[CEU][hapmap]
rs2179396	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2281039	0.82[EUR][1000 genomes]
rs2294322	0.82[EUR][1000 genomes]
rs2420512	0.82[EUR][1000 genomes]
rs2420514	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2485462	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2491087	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2491088	0.83[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2750014	0.82[MEX][hapmap]
rs2750016	0.88[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.93[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2750020	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2806382	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2806386	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2806388	0.91[CHB][hapmap];0.93[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2806393	0.87[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3753308	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs3766132	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs3766134	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs3766137	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs3766148	0.88[CEU][hapmap]
rs3766151	0.88[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs3766154	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs4508080	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs4614317	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs4615900	0.92[CEU][hapmap]
rs4656196	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs508063	0.86[CHB][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs603246	0.86[CHB][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.87[ASN][1000 genomes]
rs6427217	0.82[CEU][hapmap]
rs6427225	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs6656965	0.83[EUR][1000 genomes]
rs6670818	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6680508	0.88[CEU][hapmap]
rs6680650	0.82[EUR][1000 genomes]
rs6682835	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs6683056	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs6702969	0.81[EUR][1000 genomes]
rs717481	0.83[EUR][1000 genomes]
rs732185	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs7525259	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs7530237	0.88[CEU][hapmap]
rs7545011	0.82[EUR][1000 genomes]
rs9287097	0.88[CEU][hapmap];0.80[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2056980	C1orf112	cis	cerebellum	SCAN
rs2056980	C1orf112	Cis_1M	lymphoblastoid	RTeQTL
rs2056980	ILDR2	cis	parietal	SCAN
rs2056980	SCYL3	Cis_1M	lymphoblastoid	RTeQTL
rs2056980	ANKRD36BP1	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169872800-169887800	Weak transcription	Primary T cells from cord blood	blood
2	chr1:169875800-169889800	Weak transcription	Fetal Brain Female	brain
3	chr1:169876200-169903600	Weak transcription	Aorta	Aorta
4	chr1:169876800-169883400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:169877000-169884000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:169877600-169889800	Weak transcription	Lung	lung
7	chr1:169878400-169892200	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:169878400-169895200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr1:169878400-169946200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:169878600-169883600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:169878600-169895000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr1:169880200-169892800	Weak transcription	Fetal Heart	heart
13	chr1:169881000-169884200	Weak transcription	Pancreas	Pancrea
14	chr1:169881000-169888000	Weak transcription	Fetal Brain Male	brain
15	chr1:169881400-169901000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr1:169882200-169892000	Weak transcription	Brain Germinal Matrix	brain
17	chr1:169882400-169883600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:169882400-169883800	Enhancers	GM12878-XiMat	blood
19	chr1:169882600-169883200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr1:169882800-169886800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:169883000-169883600	Enhancers	Muscle Satellite Cultured Cells	--
22	chr1:169883000-169884000	Enhancers	NHDF-Ad	bronchial
23	chr1:169883000-169884600	Enhancers	HUVEC	blood vessel
24	chr1:169883000-169884600	Enhancers	NHEK	skin
25	chr1:169883000-169886800	Weak transcription	Fetal Stomach	stomach
26	chr1:169883000-169890600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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