Variant report

Variant	rs2405957
Chromosome Location	chr5:119950805-119950806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOS	chr5:119950226-119950846	MCF10A-Er-Src	breast:	n/a	n/a
2	PBX3	chr5:119950171-119950849	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
PRR16	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10037806	0.88[ASN][1000 genomes]
rs10053278	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10077211	0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11241557	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12054672	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12519395	0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12654348	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1375463	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1375466	0.81[CHB][hapmap]
rs1449165	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1524559	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1524564	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1960572	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2045187	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2124166	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2124167	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs2168217	0.88[ASN][1000 genomes]
rs2218717	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2405955	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4438902	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4895266	0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6881097	0.81[CHB][hapmap]
rs6881962	0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6891778	0.88[JPT][hapmap]
rs6892203	0.81[CHB][hapmap]
rs7711106	0.81[CHB][hapmap]
rs7724401	0.96[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[YRI][hapmap]
rs7735286	0.81[CHB][hapmap]
rs991672	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532200	chr5:119317901-120102513	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv830463	chr5:119806643-119968825	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031453	chr5:119843593-120393038	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv948613	chr5:119861955-119999008	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv599602	chr5:119866504-120023393	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv949499	chr5:119869763-119999008	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv830464	chr5:119950090-120106717	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:119942600-119952800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:119948200-119952000	Enhancers	Osteobl	bone
3	chr5:119948600-119952000	Enhancers	HSMM	muscle
4	chr5:119949200-119953000	Enhancers	NHLF	lung
5	chr5:119949400-119951000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr5:119949400-119951800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr5:119949400-119952400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr5:119949400-119953000	Enhancers	HMEC	breast
9	chr5:119949400-119953000	Enhancers	NHEK	skin
10	chr5:119949600-119951000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:119949600-119951200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:119949600-119951200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr5:119949600-119952000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:119949800-119951600	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr5:119949800-119953000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr5:119950000-119951000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr5:119950000-119951400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:119950200-119951000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr5:119950400-119951000	Enhancers	Primary hematopoietic stem cells	blood
20	chr5:119950600-119951000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr5:119950600-119951600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr5:119950600-119951600	Enhancers	Muscle Satellite Cultured Cells	--
23	chr5:119950600-119951600	Enhancers	NHDF-Ad	bronchial
24	chr5:119950600-119951800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:119950600-119952000	Weak transcription	Aorta	Aorta
26	chr5:119950600-119953000	Enhancers	HSMMtube	muscle
27	chr5:119950600-119954600	Weak transcription	Fetal Lung	lung
28	chr5:119950600-119967400	Weak transcription	Psoas Muscle	Psoas
29	chr5:119950800-119951600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr5:119950800-119951800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr5:119950800-119951800	Weak transcription	Brain Germinal Matrix	brain
32	chr5:119950800-119953000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:119950800-119953000	Enhancers	NH-A	brain

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