Variant report

Variant	rs17672247
Chromosome Location	chr15:30226230-30226231
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	chr15:30113575..30115417-chr15:30222883..30226780,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104067	Chromatin interaction
ENSG00000259523	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11632064	1.00[EUR][1000 genomes]
rs11634609	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs12900094	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915348	0.93[EUR][1000 genomes]
rs1474297	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28407358	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	nsv482572	chr15:30118905-30304529	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv456739	chr15:30178614-30366247	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv568716	chr15:30178614-30366247	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv431371	chr15:30193316-31012794	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
10	nsv521157	chr15:30220424-30229213	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv903756	chr15:30220424-30281105	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv1054008	chr15:30220707-30351687	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv542294	chr15:30220707-30351687	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30217400-30229200	Weak transcription	Gastric	stomach
2	chr15:30218200-30227600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:30218200-30236200	Weak transcription	Aorta	Aorta
4	chr15:30218400-30226600	Weak transcription	Brain Anterior Caudate	brain
5	chr15:30218600-30227200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:30225400-30226400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr15:30225400-30226400	Enhancers	Brain Angular Gyrus	brain
8	chr15:30225400-30226400	Enhancers	Brain Hippocampus Middle	brain
9	chr15:30225400-30226600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr15:30225400-30227000	Enhancers	Muscle Satellite Cultured Cells	--
11	chr15:30225400-30227200	Flanking Active TSS	A549	lung
12	chr15:30225400-30229200	Enhancers	Brain Cingulate Gyrus	brain
13	chr15:30225400-30230000	Enhancers	NHEK	skin
14	chr15:30225400-30231800	Enhancers	HMEC	breast
15	chr15:30225400-30232000	Enhancers	Hela-S3	cervix
16	chr15:30225600-30228000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:30225600-30230400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:30225600-30231000	Weak transcription	Esophagus	oesophagus
19	chr15:30225600-30231800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:30225800-30227000	Enhancers	Stomach Mucosa	stomach
21	chr15:30225800-30227600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:30225800-30228200	Enhancers	HUVEC	blood vessel
23	chr15:30225800-30229200	Enhancers	NHLF	lung
24	chr15:30225800-30232000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:30226000-30226400	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr15:30226000-30227400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:30226000-30227600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr15:30226000-30227800	Enhancers	HSMM	muscle
29	chr15:30226000-30228000	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr15:30226200-30227200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:30226200-30227200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr15:30226200-30227600	Enhancers	Osteobl	bone
33	chr15:30226200-30227800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:30226200-30228000	Enhancers	NH-A	brain
35	chr15:30226200-30235600	Enhancers	Brain Substantia Nigra	brain

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