Variant report

Variant	rs9827147
Chromosome Location	chr3:105162521-105162522
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:105086117..105088839-chr3:105162378..105165153,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170017	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1036581	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13100997	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2033802	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2053307	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4894924	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6790159	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7428824	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641185	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9288803	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9827196	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9864062	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9870921	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525071	chr3:105004853-105409321	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv829650	chr3:105070893-105255036	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv877304	chr3:105122214-105198374	Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
4	nsv534224	chr3:105141696-105404293	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105137400-105178600	Weak transcription	Primary B cells from cord blood	blood
2	chr3:105144400-105185000	Weak transcription	Aorta	Aorta
3	chr3:105146400-105162600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr3:105148400-105162600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr3:105150400-105163400	Weak transcription	A549	lung
6	chr3:105150800-105177800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr3:105152200-105166200	Weak transcription	Ovary	ovary
8	chr3:105155800-105177600	Weak transcription	HSMM	muscle
9	chr3:105156000-105163000	Weak transcription	NHLF	lung
10	chr3:105158000-105163200	Weak transcription	NHDF-Ad	bronchial
11	chr3:105158000-105163400	Weak transcription	Osteobl	bone
12	chr3:105159000-105165600	Weak transcription	Brain Cingulate Gyrus	brain
13	chr3:105159400-105165600	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr3:105159400-105166200	Weak transcription	Brain Hippocampus Middle	brain
15	chr3:105159400-105167400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr3:105159600-105163000	Weak transcription	Brain Anterior Caudate	brain
17	chr3:105159600-105167400	Weak transcription	Brain Angular Gyrus	brain
18	chr3:105159800-105165600	Weak transcription	Brain Substantia Nigra	brain
19	chr3:105159800-105166600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr3:105160000-105166200	Weak transcription	Liver	Liver
21	chr3:105160400-105167400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr3:105160800-105167000	Weak transcription	Fetal Heart	heart
23	chr3:105162000-105167400	Weak transcription	Gastric	stomach
24	chr3:105162200-105163000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr3:105162200-105163800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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