Variant report

Variant	rs4958024
Chromosome Location	chr5:111582288-111582289
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	chr5:111580720..111582595-chr5:111754114..111755937,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129595	Chromatin interaction
ENSG00000268358	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10037824	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10478074	0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs10478076	0.89[ASN][1000 genomes]
rs12186685	0.83[CEU][hapmap]
rs12189034	0.82[CEU][hapmap]
rs12652766	0.88[ASN][1000 genomes]
rs12655450	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12656841	0.89[ASN][1000 genomes]
rs12719140	0.89[YRI][hapmap];0.94[ASN][1000 genomes]
rs13153601	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13358904	0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[ASN][1000 genomes]
rs28620667	0.96[ASN][1000 genomes]
rs34819608	0.97[ASN][1000 genomes]
rs35005258	0.93[ASN][1000 genomes]
rs36049225	0.93[ASN][1000 genomes]
rs4323272	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs4602685	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4635975	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4958020	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4958025	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4958026	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4958029	0.88[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.90[ASN][1000 genomes]
rs56288086	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs57970031	0.99[ASN][1000 genomes]
rs59775924	0.99[ASN][1000 genomes]
rs60823180	0.97[ASN][1000 genomes]
rs61475230	0.92[ASN][1000 genomes]
rs61535569	0.97[ASN][1000 genomes]
rs62364080	0.93[ASN][1000 genomes]
rs62367266	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6594577	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs67631852	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6878423	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6879361	0.98[ASN][1000 genomes]
rs7715255	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7716479	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs9326851	0.87[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	nsv599367	chr5:110924280-111602713	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv1015302	chr5:111339022-111802947	Enhancers Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv537861	chr5:111339022-111802947	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv599368	chr5:111399885-112032675	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv948869	chr5:111476404-111695183	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv531291	chr5:111497440-111756788	Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv599371	chr5:111519018-111676755	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 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	chr5:111504800-111586400	Weak transcription	Gastric	stomach
2	chr5:111558600-111584400	Weak transcription	Psoas Muscle	Psoas
3	chr5:111558800-111591400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:111564600-111586400	Weak transcription	Lung	lung
5	chr5:111564600-111590000	Weak transcription	Left Ventricle	heart
6	chr5:111564600-111609600	Weak transcription	Pancreas	Pancrea
7	chr5:111564800-111582800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:111564800-111589400	Weak transcription	HUVEC	blood vessel
9	chr5:111567400-111602400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr5:111568600-111609600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:111569600-111589000	Weak transcription	Adipose Nuclei	Adipose
12	chr5:111572200-111584000	Weak transcription	Hela-S3	cervix
13	chr5:111572400-111582400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr5:111576200-111583600	Weak transcription	Fetal Heart	heart
15	chr5:111576200-111583800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr5:111576200-111583800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr5:111576200-111586400	Weak transcription	Esophagus	oesophagus
18	chr5:111578600-111590000	Weak transcription	Right Ventricle	heart
19	chr5:111581200-111583200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr5:111581200-111584600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:111581400-111582800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr5:111581400-111582800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:111581400-111583000	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr5:111581400-111583000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr5:111581400-111583200	Enhancers	Placenta Amnion	Placenta Amnion
26	chr5:111581600-111582800	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr5:111581600-111582800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr5:111581600-111582800	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr5:111581600-111590000	Weak transcription	Aorta	Aorta
30	chr5:111581800-111595000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr5:111582000-111583000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:111582200-111582800	Enhancers	H1 Cell Line	embryonic stem cell
33	chr5:111582200-111583200	Enhancers	Fetal Brain Male	brain

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