Variant report

Variant	rs2806386
Chromosome Location	chr1:169905532-169905533
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169903817..169906654-chr1:169908531..169910584,2	K562	blood:
2	chr1:169860365..169863802-chr1:169902105..169905662,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10733054	0.87[CEU][hapmap]
rs10737549	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs10800479	0.86[EUR][1000 genomes]
rs10800480	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs10800481	0.86[EUR][1000 genomes]
rs10800483	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs10800485	0.91[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10800486	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs10919239	0.87[CEU][hapmap]
rs10919245	0.86[EUR][1000 genomes]
rs10919248	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs10919251	0.86[EUR][1000 genomes]
rs10919263	0.85[EUR][1000 genomes]
rs12023275	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs12133843	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs12563479	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs12724797	0.91[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1330372	0.83[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap]
rs1361088	0.96[CHB][hapmap];0.91[JPT][hapmap]
rs16862933	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1883436	0.84[EUR][1000 genomes]
rs2050651	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2056980	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2056981	0.88[CEU][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs2152831	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs2179396	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs2281039	0.86[EUR][1000 genomes]
rs2294322	0.86[EUR][1000 genomes]
rs2420512	0.86[EUR][1000 genomes]
rs2420514	0.92[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2485462	0.86[EUR][1000 genomes]
rs2491087	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2491088	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2750014	0.83[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2750016	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2750020	0.86[EUR][1000 genomes]
rs2806382	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2806388	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2806393	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs2901179	1.00[YRI][hapmap]
rs3753308	0.92[CEU][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3766132	0.91[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs3766134	0.92[CEU][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs3766137	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs3766142	0.83[EUR][1000 genomes]
rs3766148	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs3766151	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs3766154	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs4141917	0.92[CEU][hapmap];0.92[CHB][hapmap];0.96[JPT][hapmap];0.83[ASN][1000 genomes]
rs4376791	0.84[EUR][1000 genomes]
rs4508080	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4614317	0.91[CEU][hapmap];0.86[EUR][1000 genomes]
rs4615900	0.88[CEU][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs4656196	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs4656203	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4656721	1.00[YRI][hapmap];0.83[EUR][1000 genomes]
rs4656725	0.83[EUR][1000 genomes]
rs6427220	0.87[CEU][hapmap]
rs6427225	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs6427228	0.80[EUR][1000 genomes]
rs6656965	0.87[EUR][1000 genomes]
rs6669794	0.83[EUR][1000 genomes]
rs6670818	0.91[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6673712	0.92[CHB][hapmap];0.91[JPT][hapmap]
rs6680508	0.84[CEU][hapmap]
rs6680650	0.86[EUR][1000 genomes]
rs6682137	0.81[EUR][1000 genomes]
rs6682835	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs6683056	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs6702969	0.85[EUR][1000 genomes]
rs717481	0.87[EUR][1000 genomes]
rs732185	0.83[CEU][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes]
rs7517490	0.84[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs7525259	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs7530237	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs7545011	0.86[EUR][1000 genomes]
rs9287097	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs9426889	0.96[CHB][hapmap];0.91[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:17 , 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	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
3	nsv1007190	chr1:169890542-169929582	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv997360	chr1:169892284-169946436	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1015110	chr1:169892661-169929582	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1013271	chr1:169892661-169960549	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010007	chr1:169895282-169946436	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1003588	chr1:169895984-169946436	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv998382	chr1:169899427-169929582	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1011978	chr1:169899427-169946436	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv997289	chr1:169899427-169960549	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1012520	chr1:169899427-169969444	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1003803	chr1:169901733-169929582	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	nsv1001670	chr1:169901733-169956450	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv1004999	chr1:169901733-169960549	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv1009843	chr1:169903077-169950341	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
17	nsv1012222	chr1:169903862-169950341	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2806386	SCYL3	Cis_1M	lymphoblastoid	RTeQTL
rs2806386	C1orf112	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169878400-169946200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr1:169884200-169913000	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr1:169885400-169913200	Weak transcription	Ovary	ovary
4	chr1:169886400-169913000	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr1:169886600-169915600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr1:169887000-169911400	Weak transcription	Left Ventricle	heart
7	chr1:169890800-169906200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr1:169891000-169911400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:169891000-169913200	Weak transcription	Adipose Nuclei	Adipose
10	chr1:169899200-169911400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:169901400-169913000	Weak transcription	Fetal Stomach	stomach
12	chr1:169901400-169913200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:169903800-169909600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:169904000-169911200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:169904000-169911400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:169904000-169929800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:169904000-169934800	Weak transcription	Fetal Heart	heart
18	chr1:169904000-169949800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:169904000-170010400	Weak transcription	Aorta	Aorta
20	chr1:169904200-169911600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:169904600-169911000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:169905200-169915400	Weak transcription	GM12878-XiMat	blood

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