Variant report

Variant	rs1489486
Chromosome Location	chr2:179684983-179684984
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:179684034..179685580-chr2:179694109..179696895,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000155657	Chromatin interaction
ENSG00000238542	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10497526	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10803920	1.00[JPT][hapmap]
rs12693171	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1489483	0.86[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565287	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2291306	1.00[CHD][hapmap]
rs4637162	1.00[JPT][hapmap]
rs4894055	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4894057	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6433738	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6707222	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6723526	1.00[CHB][hapmap]
rs6734390	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6747791	1.00[JPT][hapmap]
rs72957330	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570928	1.00[JPT][hapmap]
rs7573700	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1489486	CCDC141	cis	cerebellum	SCAN
rs1489486	TTC30A	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179659400-179698000	Weak transcription	Primary B cells from cord blood	blood
2	chr2:179674400-179691000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:179683200-179689000	Weak transcription	Left Ventricle	heart
4	chr2:179683600-179685000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr2:179683600-179685000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr2:179683600-179685000	Enhancers	HSMM	muscle
7	chr2:179683600-179685200	Enhancers	HSMMtube	muscle
8	chr2:179683600-179685800	Enhancers	Fetal Heart	heart
9	chr2:179683800-179685000	Enhancers	Muscle Satellite Cultured Cells	--
10	chr2:179683800-179685200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr2:179684200-179685000	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr2:179684200-179685000	Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr2:179684200-179685000	Enhancers	NH-A	brain
14	chr2:179684200-179685000	Enhancers	NHLF	lung
15	chr2:179684200-179685000	Enhancers	Osteobl	bone
16	chr2:179684200-179685200	Enhancers	Ovary	ovary
17	chr2:179684200-179685200	Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr2:179684200-179686000	Enhancers	Primary hematopoietic stem cells	blood
19	chr2:179684400-179685000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr2:179684400-179685000	Active TSS	Right Atrium	heart
21	chr2:179684600-179685200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr2:179684600-179685200	Flanking Active TSS	GM12878-XiMat	blood
23	chr2:179684600-179685600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:179684800-179685000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:179684800-179685000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr2:179684800-179685000	Active TSS	Aorta	Aorta
27	chr2:179684800-179685000	Enhancers	Right Ventricle	heart
28	chr2:179684800-179685200	Enhancers	Primary B cells from peripheral blood	blood
29	chr2:179684800-179685200	Enhancers	Primary T cells from cord blood	blood
30	chr2:179684800-179685200	Enhancers	Primary T cells fromperipheralblood	blood
31	chr2:179684800-179685200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
32	chr2:179684800-179685200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr2:179684800-179685200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:179684800-179685200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr2:179684800-179685200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:179684800-179685200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr2:179684800-179685200	Active TSS	Psoas Muscle	Psoas
38	chr2:179684800-179685200	Flanking Active TSS	HUVEC	blood vessel
39	chr2:179684800-179685800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr2:179684800-179685800	Enhancers	Primary T helper cells fromperipheralblood	blood

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