Variant report

Variant	rs56307541
Chromosome Location	chr15:30097368-30097369
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:30096144..30098114-chr15:30112768..30115604,2	MCF-7	breast:
2	chr15:30095523..30098044-chr15:30106073..30108934,2	MCF-7	breast:
3	chr15:30095105..30098715-chr15:30112387..30115096,4	MCF-7	breast:
4	chr15:30094465..30098543-chr15:30102930..30106302,5	K562	blood:

Variant related genes	Relation type
ENSG00000259523	Chromatin interaction
ENSG00000104067	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11632546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632848	0.88[EUR][1000 genomes]
rs11633069	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634700	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11637683	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638797	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901062	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16955758	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1719031	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1851520	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260526	0.80[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41280056	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45449102	0.83[ASN][1000 genomes]
rs45474401	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45478093	0.83[ASN][1000 genomes]
rs45505092	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45537235	0.83[ASN][1000 genomes]
rs45583033	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55845402	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719046	1.00[ASN][1000 genomes]
rs72719047	1.00[ASN][1000 genomes]
rs72719058	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719067	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719069	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72719076	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs785444	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456736	chr15:29327352-30208654	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv568675	chr15:29327352-30208654	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv995038	chr15:29744279-30366124	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1038495	chr15:29825859-30351687	Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv542293	chr15:29825859-30351687	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv832945	chr15:29932599-30123721	Genic enhancers Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
7	esv2422463	chr15:30003189-30215336	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv903754	chr15:30023454-30382120	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
9	nsv903755	chr15:30036085-30351434	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	esv1851951	chr15:30043659-30178871	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
11	esv1845759	chr15:30097078-30142373	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30058600-30106000	Weak transcription	Gastric	stomach
2	chr15:30065200-30103400	Weak transcription	Placenta	Placenta
3	chr15:30065600-30108200	Weak transcription	Pancreas	Pancrea
4	chr15:30067400-30097400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:30071800-30097600	Weak transcription	K562	blood
6	chr15:30082400-30113600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:30086000-30107600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:30086200-30097400	Weak transcription	Fetal Brain Male	brain
9	chr15:30091800-30108000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:30092000-30099600	Enhancers	Brain Hippocampus Middle	brain
11	chr15:30092200-30099200	Enhancers	Brain Cingulate Gyrus	brain
12	chr15:30092200-30099200	Enhancers	Colon Smooth Muscle	Colon
13	chr15:30092600-30111400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr15:30093000-30107600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:30093400-30098000	Enhancers	Brain Angular Gyrus	brain
16	chr15:30093400-30102600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr15:30093400-30102800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr15:30094000-30099000	Enhancers	Brain Anterior Caudate	brain
19	chr15:30094000-30099800	Enhancers	Fetal Heart	heart
20	chr15:30094200-30099400	Enhancers	Rectal Smooth Muscle	rectum
21	chr15:30094400-30098800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:30094400-30099000	Enhancers	Fetal Lung	lung
23	chr15:30094400-30099200	Enhancers	Brain Substantia Nigra	brain
24	chr15:30094600-30107600	Weak transcription	Left Ventricle	heart
25	chr15:30095200-30107000	Weak transcription	Fetal Intestine Small	intestine
26	chr15:30095600-30098200	Enhancers	Stomach Mucosa	stomach
27	chr15:30095600-30098400	Enhancers	Liver	Liver
28	chr15:30095600-30098800	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr15:30095800-30099000	Enhancers	Stomach Smooth Muscle	stomach
30	chr15:30096000-30098000	Enhancers	Muscle Satellite Cultured Cells	--
31	chr15:30096000-30098600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr15:30096200-30097800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:30096200-30097800	Enhancers	Duodenum Mucosa	Duodenum
34	chr15:30096200-30098000	Enhancers	HMEC	breast
35	chr15:30096200-30098200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:30096200-30098200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:30096200-30098800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:30096200-30099000	Enhancers	NHLF	lung
39	chr15:30096400-30098000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:30096400-30098000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:30096400-30098200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr15:30096400-30098200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr15:30096400-30098200	Enhancers	HUVEC	blood vessel
44	chr15:30096600-30097600	Enhancers	Sigmoid Colon	Sigmoid Colon
45	chr15:30096600-30098000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:30096600-30098200	Enhancers	iPS-20b Cell Line	embryonic stem cell
47	chr15:30096600-30098200	Enhancers	HSMM	muscle
48	chr15:30096600-30098600	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr15:30096600-30099000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:30096800-30097600	Enhancers	Fetal Brain Female	brain

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