Variant report

Variant	rs2399047
Chromosome Location	chr3:105217648-105217649
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	chr3:105215069..105217768-chr3:105217819..105220349,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1017915	0.88[ASW][hapmap]
rs12488738	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13080897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2062434	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28588542	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4541433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6437595	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6769329	0.86[CHB][hapmap];0.98[CHD][hapmap]
rs6804472	0.86[CHB][hapmap];0.95[CHD][hapmap]
rs7429428	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7620022	0.83[CHB][hapmap]
rs7648171	1.00[ASW][hapmap];0.90[YRI][hapmap]
rs901281	0.82[ASN][1000 genomes]
rs9810954	0.91[ASN][1000 genomes]
rs9819036	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9833101	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9833451	0.84[CHB][hapmap]
rs9843791	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843918	0.91[ASN][1000 genomes]
rs9844458	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9857705	0.86[CHB][hapmap]
rs9857961	0.86[CHB][hapmap]
rs9863750	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[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:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:105210000-105223000	Weak transcription	Gastric	stomach
2	chr3:105210200-105218400	Weak transcription	A549	lung
3	chr3:105210200-105218800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:105210200-105220600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:105210200-105220800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr3:105210200-105221200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:105210200-105222000	Weak transcription	NH-A	brain
8	chr3:105210200-105223800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:105210200-105229000	Weak transcription	HSMM	muscle
10	chr3:105210200-105243200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:105210400-105219600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr3:105210600-105218200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr3:105210600-105219600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr3:105210600-105223200	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:105210800-105222400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr3:105213800-105219600	Weak transcription	Aorta	Aorta
17	chr3:105214200-105218800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:105214200-105220000	Weak transcription	Osteobl	bone
19	chr3:105214400-105218600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr3:105214400-105219600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr3:105214400-105220600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr3:105214800-105218200	Weak transcription	HepG2	liver
23	chr3:105215000-105218600	Weak transcription	Brain Angular Gyrus	brain
24	chr3:105215400-105218200	Weak transcription	Liver	Liver
25	chr3:105215600-105218400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:105215600-105218600	Weak transcription	Brain Anterior Caudate	brain
27	chr3:105215600-105219600	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr3:105215600-105219800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:105215600-105221200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr3:105215600-105223800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:105215800-105218600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr3:105215800-105218600	Weak transcription	Fetal Lung	lung
33	chr3:105215800-105219200	Weak transcription	Brain Hippocampus Middle	brain
34	chr3:105215800-105223000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:105215800-105223200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr3:105216000-105218400	Weak transcription	Fetal Heart	heart
37	chr3:105216400-105218200	Weak transcription	Primary neutrophils fromperipheralblood	blood
38	chr3:105217400-105220200	Weak transcription	Brain Substantia Nigra	brain

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