Variant report

Variant	rs2750016
Chromosome Location	chr1:169909102-169909103
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169907968..169909649-chr1:169910615..169913475,2	K562	blood:
2	chr1:169903817..169906654-chr1:169908531..169910584,2	K562	blood:
3	chr1:169858457..169860973-chr1:169907396..169909921,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10733054	0.84[CEU][hapmap]
rs10737549	0.87[CEU][hapmap]
rs10800480	0.88[CEU][hapmap]
rs10800483	0.88[CEU][hapmap]
rs10800485	0.88[CEU][hapmap]
rs10800486	0.84[CEU][hapmap]
rs10919239	0.84[CEU][hapmap]
rs10919248	0.88[CEU][hapmap]
rs12133843	0.84[CEU][hapmap]
rs12724797	0.88[CEU][hapmap];0.81[MEX][hapmap]
rs1330372	0.80[CEU][hapmap]
rs16862831	0.89[YRI][hapmap]
rs2056980	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]
rs2056981	0.84[CEU][hapmap]
rs2179396	0.88[CEU][hapmap]
rs2420514	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2485462	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2491087	0.86[EUR][1000 genomes]
rs2491088	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2750014	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs2750020	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2806382	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2806386	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2806388	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2806393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3753308	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs3766132	0.87[CEU][hapmap]
rs3766134	0.88[CEU][hapmap]
rs3766137	0.88[CEU][hapmap]
rs3766148	0.84[CEU][hapmap]
rs3766151	0.84[CEU][hapmap]
rs3766154	0.83[CEU][hapmap]
rs4141917	0.88[CEU][hapmap]
rs4508080	0.88[CEU][hapmap]
rs4614317	0.88[CEU][hapmap]
rs4615900	0.88[CEU][hapmap]
rs4656196	0.83[CEU][hapmap]
rs508063	0.85[CHB][hapmap];0.89[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs603246	0.85[CHB][hapmap];0.86[CHD][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs6427225	0.88[CEU][hapmap]
rs6670818	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs6680508	0.84[CEU][hapmap]
rs6682835	0.88[CEU][hapmap]
rs6683056	0.87[CEU][hapmap]
rs7525259	0.84[CEU][hapmap]
rs7530237	0.84[CEU][hapmap]
rs9287097	0.84[CEU][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2750016	ANKRD36BP1	cis	parietal	SCAN
rs2750016	C1orf112	cis	cerebellum	SCAN
rs2750016	ILDR2	cis	parietal	SCAN
rs2750016	PKD2L1	trans	parietal	SCAN

Chromatin state (count:23 , 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	chr1:169891000-169911400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:169891000-169913200	Weak transcription	Adipose Nuclei	Adipose
9	chr1:169899200-169911400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr1:169901400-169913000	Weak transcription	Fetal Stomach	stomach
11	chr1:169901400-169913200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr1:169903800-169909600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:169904000-169911200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr1:169904000-169911400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:169904000-169929800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:169904000-169934800	Weak transcription	Fetal Heart	heart
17	chr1:169904000-169949800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:169904000-170010400	Weak transcription	Aorta	Aorta
19	chr1:169904200-169911600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:169904600-169911000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:169905200-169915400	Weak transcription	GM12878-XiMat	blood
22	chr1:169907800-169913200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:169908200-169909600	Weak transcription	Esophagus	oesophagus

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