Variant report

Variant	rs10055530
Chromosome Location	chr5:1952404-1952405
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:1799852..1801806-chr5:1950738..1953312,2	MCF-7	breast:
2	chr5:1799132..1801458-chr5:1950722..1953001,2	K562	blood:

Variant related genes	Relation type
ENSG00000171421	Chromatin interaction
ENSG00000145494	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10055535	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10055976	1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs10057823	0.88[AFR][1000 genomes]
rs10067670	0.86[EUR][1000 genomes]
rs10073095	0.90[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13356887	0.86[EUR][1000 genomes]
rs13361234	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16902204	0.86[EUR][1000 genomes]
rs2087139	0.86[EUR][1000 genomes]
rs2087140	0.86[EUR][1000 genomes]
rs28394513	0.96[AFR][1000 genomes]
rs28408700	1.00[EUR][1000 genomes]
rs2883062	1.00[EUR][1000 genomes]
rs4975773	0.94[AFR][1000 genomes]
rs55989314	0.86[EUR][1000 genomes]
rs57133261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58615662	0.86[EUR][1000 genomes]
rs6861498	0.86[EUR][1000 genomes]
rs6863193	0.80[EUR][1000 genomes]
rs6863375	0.86[EUR][1000 genomes]
rs73732507	0.86[EUR][1000 genomes]
rs73735137	0.86[EUR][1000 genomes]
rs73735140	0.86[EUR][1000 genomes]
rs73735141	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817407	chr5:1495354-2191460	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	107 gene(s)	inside rSNPs	diseases
2	nsv869236	chr5:1719263-2259100	Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv915846	chr5:1891098-2167677	Active TSS Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1026930	chr5:1898993-2126061	Bivalent/Poised TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv508344	chr5:1905222-1976860	Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv881562	chr5:1907974-1976187	Enhancers Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv880964	chr5:1912921-1953161	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv3389807	chr5:1949052-1953850	Weak transcription ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv3405956	chr5:1950352-1952450	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	nsv427705	chr5:1950467-2115059	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:1939000-1965600	Weak transcription	Brain Angular Gyrus	brain
2	chr5:1942600-1953800	Weak transcription	Ovary	ovary
3	chr5:1949800-1960600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr5:1950600-1963800	Weak transcription	Right Ventricle	heart
5	chr5:1951400-1953200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr5:1951400-1954000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr5:1951800-1952600	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr5:1951800-1953200	Enhancers	H9 Cell Line	embryonic stem cell
9	chr5:1951800-1961400	Weak transcription	HMEC	breast
10	chr5:1952000-1952600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr5:1952000-1952600	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr5:1952000-1953000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr5:1952000-1953200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr5:1952000-1953200	Enhancers	Fetal Heart	heart
15	chr5:1952000-1953200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr5:1952000-1953400	Enhancers	H1 Cell Line	embryonic stem cell
17	chr5:1952000-1960600	Weak transcription	Gastric	stomach
18	chr5:1952000-1960600	Weak transcription	Pancreas	Pancrea
19	chr5:1952200-1952800	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr5:1952200-1953200	Bivalent Enhancer	Fetal Muscle Leg	muscle
21	chr5:1952200-1953400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr5:1952200-1953400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
23	chr5:1952200-1953400	Bivalent Enhancer	Fetal Stomach	stomach
24	chr5:1952200-1953800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr5:1952200-1962000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:1952200-1962200	Weak transcription	NHEK	skin
27	chr5:1952400-1952600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr5:1952400-1952600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr5:1952400-1952800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:1952400-1953000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:1952400-1953400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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