Variant report

Variant	rs13228854
Chromosome Location	chr7:5488045-5488046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:5481781..5483305-chr7:5487819..5490251,2	MCF-7	breast:
2	chr7:5460548..5470879-chr7:5485628..5502297,36	K562	blood:
3	chr7:5479996..5482782-chr7:5485785..5488364,2	K562	blood:
4	chr7:5486211..5489791-chr7:5490283..5493222,3	K562	blood:
5	chr7:5463779..5472786-chr7:5487740..5494468,14	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272953	Chromatin interaction
ENSG00000182095	Chromatin interaction
ENSG00000234432	Chromatin interaction
ENSG00000273084	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs13223393	0.89[ASN][1000 genomes]
rs13228277	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34708501	0.97[ASN][1000 genomes]
rs35606034	0.81[EUR][1000 genomes]
rs4298402	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4724684	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6463479	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6957693	0.86[ASN][1000 genomes]
rs6957701	0.85[ASN][1000 genomes]
rs6961855	0.82[EUR][1000 genomes]
rs6979161	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	nsv887391	chr7:5224407-5572132	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	292 gene(s)	inside rSNPs	diseases
5	esv1814049	chr7:5314993-5675131	Active TSS Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	333 gene(s)	inside rSNPs	diseases
6	esv1820266	chr7:5332088-5665173	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	332 gene(s)	inside rSNPs	diseases
7	nsv533965	chr7:5370746-5548397	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
8	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
9	nsv887401	chr7:5393243-5539958	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
10	nsv887402	chr7:5394951-5494677	Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv887404	chr7:5402606-5667645	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
12	nsv887405	chr7:5409059-5552436	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
13	nsv887406	chr7:5414602-5552436	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	52 gene(s)	inside rSNPs	diseases
14	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
15	nsv887407	chr7:5432672-5605130	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	302 gene(s)	inside rSNPs	diseases
16	nsv887408	chr7:5432672-5667645	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	331 gene(s)	inside rSNPs	diseases
17	nsv508443	chr7:5447283-5501122	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
18	nsv526194	chr7:5452756-5592436	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	278 gene(s)	inside rSNPs	diseases
19	nsv830890	chr7:5464933-5705158	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
20	nsv984498	chr7:5469767-5506036	Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv887409	chr7:5477922-5539958	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
22	esv3422617	chr7:5486026-5488174	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
23	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5470200-5491800	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr7:5470400-5497600	Weak transcription	Right Atrium	heart
3	chr7:5473200-5491200	Weak transcription	Hela-S3	cervix
4	chr7:5473200-5497200	Weak transcription	Right Ventricle	heart
5	chr7:5480000-5490200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr7:5483400-5490000	Weak transcription	Primary hematopoietic stem cells	blood
7	chr7:5483600-5489800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:5483800-5488200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr7:5483800-5490800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:5484000-5490200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr7:5484000-5491600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr7:5485600-5489400	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr7:5486000-5490200	Weak transcription	Brain Anterior Caudate	brain
14	chr7:5486000-5490600	Weak transcription	Brain Substantia Nigra	brain
15	chr7:5486200-5488200	Weak transcription	Fetal Brain Male	brain
16	chr7:5486200-5490200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr7:5486200-5490200	Weak transcription	Stomach Mucosa	stomach
18	chr7:5486400-5490200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr7:5486400-5490600	Weak transcription	A549	lung
20	chr7:5486600-5488200	Weak transcription	Fetal Thymus	thymus
21	chr7:5486600-5490200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:5486600-5490200	Weak transcription	Fetal Intestine Large	intestine
23	chr7:5486600-5490200	Weak transcription	Fetal Intestine Small	intestine
24	chr7:5486600-5490400	Weak transcription	Ovary	ovary
25	chr7:5486600-5491200	Weak transcription	Spleen	Spleen
26	chr7:5486600-5497200	Weak transcription	Lung	lung
27	chr7:5486800-5488400	Weak transcription	Brain Hippocampus Middle	brain
28	chr7:5486800-5490000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr7:5487200-5488800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr7:5487400-5488800	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr7:5487400-5489400	Enhancers	Placenta	Placenta
32	chr7:5487600-5488600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr7:5487600-5488800	Enhancers	H1 Cell Line	embryonic stem cell
34	chr7:5487600-5488800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:5487600-5488800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:5487600-5488800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:5487600-5488800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr7:5487600-5488800	Enhancers	Brain Germinal Matrix	brain
39	chr7:5487600-5489400	Enhancers	Esophagus	oesophagus
40	chr7:5487600-5490200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr7:5487800-5488800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr7:5487800-5488800	Enhancers	HMEC	breast
43	chr7:5487800-5495200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr7:5488000-5488200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr7:5488000-5488200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr7:5488000-5488400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr7:5488000-5488400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr7:5488000-5488400	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr7:5488000-5488400	Weak transcription	Fetal Brain Female	brain
50	chr7:5488000-5488600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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