Variant report

Variant	rs7162504
Chromosome Location	chr15:55954118-55954119
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55951550..55954249-chr15:56034622..56036474,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166450	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16976467	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16976472	0.93[YRI][hapmap]
rs17238367	0.93[YRI][hapmap]
rs28428526	0.81[AFR][1000 genomes]
rs28481986	0.81[AFR][1000 genomes]
rs28557162	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28576513	0.83[AFR][1000 genomes]
rs28621834	0.81[AFR][1000 genomes]
rs4774220	0.80[AFR][1000 genomes]
rs6493806	1.00[CEU][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162879	0.93[YRI][hapmap]
rs7164032	0.91[AFR][1000 genomes]
rs7176699	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7179697	1.00[YRI][hapmap]
rs8030790	0.82[ASN][1000 genomes]
rs8032175	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs9920546	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv457158	chr15:55930542-55982257	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv569541	chr15:55930542-55982257	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 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	chr15:55911800-55977000	Weak transcription	Fetal Intestine Small	intestine
2	chr15:55920800-55987600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:55932600-55987000	Weak transcription	Ovary	ovary
4	chr15:55932800-55973400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:55942800-55974400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:55947400-55960200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:55951200-55955400	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr15:55951200-55956000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:55951400-55955600	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr15:55952000-55955200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:55952200-55960000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:55952400-55954400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr15:55952400-55954600	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr15:55952400-55955800	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr15:55952400-55957000	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:55952800-55955400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:55952800-55972000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:55953200-55954200	Enhancers	Fetal Lung	lung
19	chr15:55953200-55954400	Enhancers	HepG2	liver
20	chr15:55953200-55955400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr15:55953400-55954200	Enhancers	Fetal Intestine Large	intestine
22	chr15:55953400-55954200	Enhancers	NH-A	brain
23	chr15:55953400-55954400	Enhancers	H1 Cell Line	embryonic stem cell
24	chr15:55953400-55954400	Enhancers	Hela-S3	cervix
25	chr15:55953400-55954600	Enhancers	A549	lung
26	chr15:55953400-55955400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:55953600-55954200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr15:55953600-55954600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr15:55953800-55955200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:55953800-55955400	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr15:55953800-55964800	Weak transcription	Right Ventricle	heart
32	chr15:55954000-55954400	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr15:55954000-55955000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:55954000-55955600	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr15:55954000-55968600	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr15:55954000-55971600	Weak transcription	Fetal Kidney	kidney
37	chr15:55954000-55975400	Weak transcription	HSMM	muscle
38	chr15:55954000-55977400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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