Variant report

Variant	rs1489484
Chromosome Location	chr2:179685144-179685145
allele	A/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
ENSG00000238542	Chromatin interaction
ENSG00000155657	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10165253	0.93[JPT][hapmap]
rs10189747	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10190488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210964	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10930835	0.88[ASN][1000 genomes]
rs10930836	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11885885	0.89[ASN][1000 genomes]
rs11886281	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11897189	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12615288	0.87[EUR][1000 genomes]
rs13417557	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1489482	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2046777	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2078403	0.80[JPT][hapmap]
rs2086832	0.93[JPT][hapmap]
rs2129108	1.00[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2170850	0.94[JPT][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2220127	0.93[JPT][hapmap]
rs4292125	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4893855	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56988799	0.89[ASN][1000 genomes]
rs59415652	0.88[ASN][1000 genomes]
rs7590740	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs998329	1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]

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

No data

Chromatin state (count:35 , 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	chr2:179683600-179685200	Enhancers	HSMMtube	muscle
5	chr2:179683600-179685800	Enhancers	Fetal Heart	heart
6	chr2:179683800-179685200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:179684200-179685200	Enhancers	Ovary	ovary
8	chr2:179684200-179685200	Active TSS	Skeletal Muscle Female	skeletal muscle
9	chr2:179684200-179686000	Enhancers	Primary hematopoietic stem cells	blood
10	chr2:179684600-179685200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:179684600-179685200	Flanking Active TSS	GM12878-XiMat	blood
12	chr2:179684600-179685600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr2:179684800-179685200	Enhancers	Primary B cells from peripheral blood	blood
14	chr2:179684800-179685200	Enhancers	Primary T cells from cord blood	blood
15	chr2:179684800-179685200	Enhancers	Primary T cells fromperipheralblood	blood
16	chr2:179684800-179685200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
17	chr2:179684800-179685200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr2:179684800-179685200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr2:179684800-179685200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr2:179684800-179685200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:179684800-179685200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:179684800-179685200	Active TSS	Psoas Muscle	Psoas
23	chr2:179684800-179685200	Flanking Active TSS	HUVEC	blood vessel
24	chr2:179684800-179685800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr2:179684800-179685800	Enhancers	Primary T helper cells fromperipheralblood	blood
26	chr2:179685000-179685200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr2:179685000-179685200	Flanking Active TSS	Aorta	Aorta
28	chr2:179685000-179685600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr2:179685000-179688800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr2:179685000-179689400	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:179685000-179689600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr2:179685000-179689600	Weak transcription	Osteobl	bone
33	chr2:179685000-179692600	Weak transcription	Right Ventricle	heart
34	chr2:179685000-179693800	Weak transcription	HSMM	muscle
35	chr2:179685000-179694000	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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