Variant report

Variant	rs9846152
Chromosome Location	chr3:105232816-105232817
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	chr3:105085752..105088107-chr3:105232298..105234295,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170017	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs10446293	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6776462	0.84[CHB][hapmap]
rs7613684	0.81[CHB][hapmap];0.96[CHD][hapmap]
rs7613790	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs901279	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9283550	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9288810	1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	nsv829651	chr3:105203424-105402136	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
5	nsv460811	chr3:105212993-105316769	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv591240	chr3:105212993-105316769	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105210200-105243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr3:105221400-105300400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:105222200-105260600	Weak transcription	Fetal Kidney	kidney
4	chr3:105222800-105246000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:105223800-105274800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:105224400-105239600	Weak transcription	GM12878-XiMat	blood
7	chr3:105225800-105236000	Weak transcription	Liver	Liver
8	chr3:105227400-105233800	Weak transcription	Brain Substantia Nigra	brain
9	chr3:105228800-105233200	Enhancers	Osteobl	bone
10	chr3:105229400-105233200	Enhancers	NHDF-Ad	bronchial
11	chr3:105229600-105244600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr3:105229600-105260400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr3:105229800-105233000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:105229800-105233200	Enhancers	Muscle Satellite Cultured Cells	--
15	chr3:105229800-105235000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr3:105230000-105233400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr3:105230000-105234200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr3:105230200-105262600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:105230400-105234200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr3:105230600-105233800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:105230800-105234200	Weak transcription	Brain Angular Gyrus	brain
22	chr3:105231000-105237400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:105231400-105234200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:105231600-105233400	Enhancers	HSMM	muscle
25	chr3:105231800-105233200	Enhancers	HMEC	breast
26	chr3:105231800-105234600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr3:105232000-105234600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr3:105232200-105233000	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr3:105232200-105233000	Enhancers	Brain Anterior Caudate	brain
30	chr3:105232200-105233000	Weak transcription	A549	lung
31	chr3:105232200-105233600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:105232200-105245400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr3:105232200-105245400	Weak transcription	NHEK	skin
34	chr3:105232200-105245600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:105232200-105274000	Weak transcription	HSMMtube	muscle
36	chr3:105232400-105233600	Weak transcription	Brain Hippocampus Middle	brain
37	chr3:105232400-105237600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr3:105232400-105237600	Weak transcription	Fetal Heart	heart
39	chr3:105232600-105234200	Weak transcription	Brain Cingulate Gyrus	brain
40	chr3:105232600-105242400	Weak transcription	NHLF	lung
41	chr3:105232800-105236000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:105232800-105243200	Weak transcription	NH-A	brain

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