Variant report

Variant	rs17524415
Chromosome Location	chr15:51673382-51673383
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:30 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:51581375..51582062-chr15:51673145..51673669,2	MCF-7	breast:
2	chr15:51578027..51580996-chr15:51672826..51674102,51	MCF-7	breast:
3	chr15:51574618..51575812-chr15:51673135..51674386,4	MCF-7	breast:
4	chr15:51454926..51455797-chr15:51673153..51673909,4	MCF-7	breast:
5	chr15:51571944..51572724-chr15:51673082..51674003,2	MCF-7	breast:
6	chr15:51672962..51673958-chr15:51793026..51793755,2	MCF-7	breast:
7	chr15:51484722..51485709-chr15:51673245..51674090,4	MCF-7	breast:
8	chr15:51573015..51575119-chr15:51672522..51674124,19	MCF-7	breast:
9	chr15:51672133..51674864-chr15:51676957..51679239,3	MCF-7	breast:
10	chr15:51571217..51573102-chr15:51670721..51673582,2	MCF-7	breast:
11	chr15:51666614..51670918-chr15:51672789..51675914,5	MCF-7	breast:
12	chr15:51578343..51581420-chr15:51671893..51675869,118	MCF-7	breast:
13	chr15:51654951..51657381-chr15:51671722..51675583,3	K562	blood:
14	chr15:51634192..51635133-chr15:51673006..51674097,3	MCF-7	breast:
15	chr15:51454781..51456161-chr15:51672829..51674093,16	MCF-7	breast:
16	chr15:51521683..51523423-chr15:51672827..51674183,15	MCF-7	breast:
17	chr15:51591182..51591700-chr15:51673143..51673644,2	MCF-7	breast:
18	chr15:51521787..51522680-chr15:51673138..51674597,7	MCF-7	breast:
19	chr15:51633014..51633734-chr15:51672778..51673632,2	MCF-7	breast:
20	chr15:51573305..51574299-chr15:51673096..51674022,6	K562	blood:
21	chr15:51591665..51592522-chr15:51673148..51674027,2	MCF-7	breast:
22	chr15:51455012..51455878-chr15:51673133..51674169,7	K562	blood:
23	chr15:51658520..51659654-chr15:51673214..51673922,3	MCF-7	breast:
24	chr15:51577066..51580410-chr15:51672799..51675704,3	MCF-7	breast:
25	chr15:51573150..51574316-chr15:51672564..51674447,46	MCF-7	breast:
26	chr15:51604419..51605525-chr15:51673233..51674014,3	MCF-7	breast:
27	chr12:49523938..49524712-chr15:51673098..51673696,2	MCF-7	breast:
28	chr15:51668522..51670748-chr15:51671357..51673497,2	K562	blood:
29	chr15:51425244..51425785-chr15:51673112..51674004,3	MCF-7	breast:
30	chr15:51673157..51673657-chr17:59494266..59494829,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000186417	Chromatin interaction
ENSG00000259701	Chromatin interaction
ENSG00000259194	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1001864	1.00[ASW][hapmap];1.00[CEU][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17647707	1.00[ASW][hapmap]
rs28757159	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
4	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
7	nsv904216	chr15:51631479-51739808	Bivalent Enhancer Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17524415	RASA1	trans	parietal	SCAN
rs17524415	GLDN	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51640800-51676200	Weak transcription	Aorta	Aorta
2	chr15:51660200-51676200	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr15:51665600-51674200	Enhancers	Brain Hippocampus Middle	brain
4	chr15:51668000-51679000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:51669400-51674800	Weak transcription	Osteobl	bone
6	chr15:51670200-51674400	Enhancers	Brain Angular Gyrus	brain
7	chr15:51670200-51675200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr15:51670400-51674000	Enhancers	Brain Anterior Caudate	brain
9	chr15:51670800-51673600	Enhancers	Stomach Smooth Muscle	stomach
10	chr15:51670800-51674400	Enhancers	Brain Inferior Temporal Lobe	brain
11	chr15:51671000-51674400	Enhancers	Brain Cingulate Gyrus	brain
12	chr15:51671200-51673600	Enhancers	Adipose Nuclei	Adipose
13	chr15:51671600-51673600	Enhancers	Stomach Mucosa	stomach
14	chr15:51671800-51673400	Weak transcription	Fetal Lung	lung
15	chr15:51672000-51673600	Enhancers	Placenta	Placenta
16	chr15:51672400-51673600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr15:51672400-51675200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr15:51672400-51678000	Weak transcription	Lung	lung
19	chr15:51672600-51673400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr15:51672600-51673600	Enhancers	Fetal Muscle Leg	muscle
21	chr15:51672600-51676400	Weak transcription	Brain Germinal Matrix	brain
22	chr15:51672600-51691000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:51672800-51673800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:51673200-51673400	Enhancers	Liver	Liver
25	chr15:51673200-51673400	Enhancers	Fetal Heart	heart
26	chr15:51673200-51673400	Active TSS	Rectal Smooth Muscle	rectum
27	chr15:51673200-51673400	Enhancers	A549	lung
28	chr15:51673200-51673600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr15:51673200-51673600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:51673200-51673600	Flanking Active TSS	Brain Substantia Nigra	brain
31	chr15:51673200-51673600	Enhancers	Colon Smooth Muscle	Colon
32	chr15:51673200-51673600	Enhancers	Fetal Stomach	stomach
33	chr15:51673200-51673600	Enhancers	Skeletal Muscle Female	skeletal muscle
34	chr15:51673200-51673600	Enhancers	HepG2	liver
35	chr15:51673200-51673600	Bivalent Enhancer	HUVEC	blood vessel
36	chr15:51673200-51673600	Enhancers	K562	blood
37	chr15:51673200-51673600	Enhancers	NHDF-Ad	bronchial

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