Variant report

Variant	rs998329
Chromosome Location	chr2:179684239-179684240
allele	A/G
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: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10165253	0.94[JPT][hapmap]
rs10184892	1.00[CEU][hapmap];0.95[CHB][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10189747	0.97[ASN][1000 genomes]
rs10190488	1.00[JPT][hapmap];0.80[YRI][hapmap];0.88[ASN][1000 genomes]
rs10199751	0.81[JPT][hapmap]
rs10210964	0.86[ASN][1000 genomes]
rs10930835	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10930836	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11885885	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11886281	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11897189	0.82[ASN][1000 genomes]
rs13417557	0.93[ASN][1000 genomes]
rs13420249	1.00[CEU][hapmap]
rs1489482	0.83[ASN][1000 genomes]
rs1489484	1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2046777	0.88[ASN][1000 genomes]
rs2078403	0.81[JPT][hapmap]
rs2086832	0.94[JPT][hapmap]
rs2129108	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2170850	1.00[CEU][hapmap];0.85[CHB][hapmap];0.94[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2220127	0.94[JPT][hapmap]
rs2279472	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs4292125	0.84[ASN][1000 genomes]
rs4893855	0.96[ASN][1000 genomes]
rs56988799	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59415652	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73040346	0.84[EUR][1000 genomes]
rs7590740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179646000-179684800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr2:179659400-179698000	Weak transcription	Primary B cells from cord blood	blood
3	chr2:179666800-179684800	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr2:179674400-179691000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:179676400-179684400	Weak transcription	Psoas Muscle	Psoas
6	chr2:179681400-179684800	Weak transcription	Primary T cells from cord blood	blood
7	chr2:179682200-179684400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr2:179682600-179684400	Weak transcription	GM12878-XiMat	blood
9	chr2:179683200-179689000	Weak transcription	Left Ventricle	heart
10	chr2:179683600-179685000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:179683600-179685000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:179683600-179685000	Enhancers	HSMM	muscle
13	chr2:179683600-179685200	Enhancers	HSMMtube	muscle
14	chr2:179683600-179685800	Enhancers	Fetal Heart	heart
15	chr2:179683800-179685000	Enhancers	Muscle Satellite Cultured Cells	--
16	chr2:179683800-179685200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:179684000-179684800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:179684200-179684600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr2:179684200-179684600	Enhancers	NHDF-Ad	bronchial
20	chr2:179684200-179684800	Enhancers	HUVEC	blood vessel
21	chr2:179684200-179685000	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr2:179684200-179685000	Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr2:179684200-179685000	Enhancers	NH-A	brain
24	chr2:179684200-179685000	Enhancers	NHLF	lung
25	chr2:179684200-179685000	Enhancers	Osteobl	bone
26	chr2:179684200-179685200	Enhancers	Ovary	ovary
27	chr2:179684200-179685200	Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr2:179684200-179686000	Enhancers	Primary hematopoietic stem cells	blood

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