Variant report

Variant	rs2750014
Chromosome Location	chr1:169903077-169903078
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169883530..169886106-chr1:169901752..169904376,3	K562	blood:
2	chr1:169898316..169900651-chr1:169903000..169904751,2	K562	blood:
3	chr1:169860365..169863802-chr1:169902105..169905662,4	MCF-7	breast:
4	chr1:169887846..169894353-chr1:169898169..169903456,7	K562	blood:

Variant related genes	Relation type
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10800485	0.85[MEX][hapmap]
rs12023275	0.82[JPT][hapmap]
rs12563479	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs12724797	0.84[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.86[ASN][1000 genomes]
rs1330372	0.83[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap]
rs1361088	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs16862933	1.00[ASW][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap]
rs1883437	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2050651	0.87[CHB][hapmap];0.86[JPT][hapmap];0.85[MEX][hapmap]
rs2056980	0.82[MEX][hapmap]
rs2152831	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs2491087	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2750016	0.80[CEU][hapmap];0.82[MEX][hapmap]
rs2806386	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]
rs4141917	0.84[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs4656203	0.85[CHB][hapmap];0.84[CHD][hapmap]
rs6670818	0.85[MEX][hapmap];0.80[TSI][hapmap]
rs6673712	0.83[CHB][hapmap];0.86[JPT][hapmap]
rs7517490	0.83[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap]
rs7519364	0.84[EUR][1000 genomes]
rs9426889	0.87[CHB][hapmap];0.85[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	nsv947333	chr1:169899109-169903291	Enhancers Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2750014	C1orf112	Cis_1M	lymphoblastoid	RTeQTL
rs2750014	C1orf112	cis	cerebellum	SCAN
rs2750014	GPA33	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169876200-169903600	Weak transcription	Aorta	Aorta
2	chr1:169878400-169946200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr1:169884200-169913000	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:169885400-169913200	Weak transcription	Ovary	ovary
5	chr1:169885600-169903200	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:169886400-169913000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr1:169886600-169915600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr1:169887000-169911400	Weak transcription	Left Ventricle	heart
9	chr1:169890800-169906200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr1:169891000-169911400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr1:169891000-169913200	Weak transcription	Adipose Nuclei	Adipose
12	chr1:169894200-169903400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:169899200-169911400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr1:169901400-169903200	Weak transcription	Fetal Heart	heart
15	chr1:169901400-169903200	Weak transcription	Fetal Kidney	kidney
16	chr1:169901400-169903200	Weak transcription	Fetal Lung	lung
17	chr1:169901400-169903600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr1:169901400-169913000	Weak transcription	Fetal Stomach	stomach
19	chr1:169901400-169913200	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr1:169901600-169903200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr1:169901800-169903200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:169901800-169903400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:169902600-169904000	Enhancers	Hela-S3	cervix
24	chr1:169902800-169903200	Weak transcription	NHLF	lung
25	chr1:169902800-169904000	Enhancers	NHDF-Ad	bronchial
26	chr1:169903000-169903800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:169903000-169904000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:169903000-169904000	Enhancers	Osteobl	bone
29	chr1:169903000-169904200	Enhancers	NH-A	brain

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