Variant report

Variant	rs12594461
Chromosome Location	chr15:30210231-30210232
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:30208802..30211048-chr15:30212481..30214180,2	MCF-7	breast:

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1001877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12592270	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594438	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1357386	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1357387	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1357388	0.84[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[ASN][1000 genomes]
rs1357389	0.84[ASN][1000 genomes]
rs1403355	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1464564	0.84[ASN][1000 genomes]
rs1464565	0.84[ASN][1000 genomes]
rs1522640	0.84[ASN][1000 genomes]
rs1522643	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1522791	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1522792	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1522794	0.97[ASN][1000 genomes]
rs1533860	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1631472	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1632356	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1718977	0.84[ASN][1000 genomes]
rs1718985	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1718986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1718987	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1718988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1718989	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1718990	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1718991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1718993	0.96[ASN][1000 genomes]
rs1718997	0.92[ASN][1000 genomes]
rs1718998	0.95[ASN][1000 genomes]
rs1718999	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1719001	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1719040	0.84[ASN][1000 genomes]
rs1719041	0.84[ASN][1000 genomes]
rs1719337	0.99[ASN][1000 genomes]
rs1719338	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1719341	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1719343	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1719345	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1719348	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1719349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1719350	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1719351	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1719352	0.97[ASN][1000 genomes]
rs1719353	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1719354	0.96[ASN][1000 genomes]
rs1719358	0.97[ASN][1000 genomes]
rs1719359	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1719360	0.97[ASN][1000 genomes]
rs1719361	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1719363	0.96[EUR][1000 genomes]
rs1879895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2103056	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2253906	0.97[ASN][1000 genomes]
rs2461657	0.91[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2948555	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34866689	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4503741	0.82[ASN][1000 genomes]
rs4779461	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4779672	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4779673	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4779674	1.00[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4779675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4779677	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4779681	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72625154	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs939976	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs939977	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939978	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][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	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	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
5	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
6	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
7	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
8	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
9	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
10	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

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30206400-30212400	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr15:30206800-30211400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr15:30206800-30216400	Weak transcription	HSMM	muscle
4	chr15:30207000-30212600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:30207000-30212600	Weak transcription	Placenta	Placenta
6	chr15:30207200-30211400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:30207200-30211400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr15:30207200-30211800	Weak transcription	Lung	lung
9	chr15:30207200-30212000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr15:30207200-30212200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr15:30207200-30212200	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:30207200-30212400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:30207200-30212600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:30207200-30212800	Weak transcription	Pancreas	Pancrea
15	chr15:30207200-30213000	Weak transcription	Right Ventricle	heart
16	chr15:30207200-30213800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr15:30207200-30216400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr15:30207200-30216800	Weak transcription	Fetal Kidney	kidney
19	chr15:30207400-30210800	Weak transcription	Brain Anterior Caudate	brain
20	chr15:30209200-30210400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr15:30209200-30210600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:30209200-30210800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:30209200-30213800	Enhancers	Brain Inferior Temporal Lobe	brain
24	chr15:30209400-30210400	Enhancers	NH-A	brain
25	chr15:30209400-30210600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr15:30209600-30210400	Enhancers	NHLF	lung
27	chr15:30209600-30210600	Flanking Active TSS	A549	lung
28	chr15:30209600-30210600	Enhancers	NHEK	skin
29	chr15:30209600-30210600	Enhancers	Osteobl	bone
30	chr15:30209800-30210400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr15:30209800-30210400	Enhancers	HMEC	breast
32	chr15:30209800-30210400	Enhancers	NHDF-Ad	bronchial
33	chr15:30209800-30210600	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr15:30209800-30210600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:30209800-30210600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr15:30209800-30210800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:30209800-30210800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:30210000-30210400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:30210000-30210400	Enhancers	Hela-S3	cervix
40	chr15:30210000-30211000	Weak transcription	Brain Hippocampus Middle	brain
41	chr15:30210000-30211200	Weak transcription	Brain Angular Gyrus	brain
42	chr15:30210000-30211200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr15:30210000-30211200	Weak transcription	Brain Substantia Nigra	brain
44	chr15:30210000-30211400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr15:30210000-30212000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:30210000-30212000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr15:30210000-30212600	Weak transcription	Fetal Heart	heart
48	chr15:30210000-30213600	Weak transcription	Esophagus	oesophagus
49	chr15:30210200-30210400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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