Variant report

Variant	rs939978
Chromosome Location	chr15:30216397-30216398
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:30111488..30116062-chr15:30215235..30221223,14	MCF-7	breast:
2	chr15:30111263..30115362-chr15:30215775..30219820,11	MCF-7	breast:
3	chr15:30040269..30041825-chr15:30216236..30217784,2	MCF-7	breast:
4	chr15:30213326..30217434-chr15:30217608..30221086,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104067	Chromatin interaction
ENSG00000259523	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1001877	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592270	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12594438	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12594461	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1357386	0.98[ASN][1000 genomes]
rs1357387	0.98[ASN][1000 genomes]
rs1357388	0.98[ASN][1000 genomes]
rs1357389	0.83[ASN][1000 genomes]
rs1403355	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1464564	0.84[ASN][1000 genomes]
rs1464565	0.84[ASN][1000 genomes]
rs1522640	0.84[ASN][1000 genomes]
rs1522643	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1522791	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1522792	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1522794	0.98[ASN][1000 genomes]
rs1533860	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1631472	0.98[ASN][1000 genomes]
rs1632356	0.98[ASN][1000 genomes]
rs1718977	0.84[ASN][1000 genomes]
rs1718985	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1718986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1718987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1718988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1718989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1718990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1718991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1718993	0.98[ASN][1000 genomes]
rs1718997	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1718998	0.97[ASN][1000 genomes]
rs1718999	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1719001	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1719040	0.84[ASN][1000 genomes]
rs1719041	0.84[ASN][1000 genomes]
rs1719337	0.98[ASN][1000 genomes]
rs1719338	0.98[ASN][1000 genomes]
rs1719341	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1719343	0.99[ASN][1000 genomes]
rs1719345	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1719348	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1719349	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1719350	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1719351	0.98[ASN][1000 genomes]
rs1719352	0.98[ASN][1000 genomes]
rs1719353	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1719354	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1719358	0.98[ASN][1000 genomes]
rs1719359	0.98[ASN][1000 genomes]
rs1719360	0.98[ASN][1000 genomes]
rs1719361	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1719363	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2103056	0.98[ASN][1000 genomes]
rs2253906	0.98[ASN][1000 genomes]
rs2461657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2948555	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34866689	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4503741	0.83[ASN][1000 genomes]
rs4779461	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4779672	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4779673	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4779674	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4779675	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4779676	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4779677	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4779681	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72625154	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs939976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs939977	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:30206800-30216400	Weak transcription	HSMM	muscle
2	chr15:30207200-30216400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr15:30207200-30216800	Weak transcription	Fetal Kidney	kidney
4	chr15:30212800-30216600	Weak transcription	Brain Substantia Nigra	brain
5	chr15:30213000-30216400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr15:30213000-30216800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:30213000-30216800	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:30213200-30216400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:30213400-30217200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr15:30213400-30218800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:30213800-30216400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr15:30213800-30216400	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:30213800-30216400	Weak transcription	Left Ventricle	heart
14	chr15:30213800-30216600	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr15:30213800-30216600	Weak transcription	Hela-S3	cervix
16	chr15:30213800-30216800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr15:30213800-30216800	Weak transcription	Brain Angular Gyrus	brain
18	chr15:30213800-30216800	Weak transcription	Lung	lung
19	chr15:30213800-30217000	Weak transcription	Brain Anterior Caudate	brain
20	chr15:30213800-30217000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:30213800-30217000	Weak transcription	Pancreas	Pancrea
22	chr15:30213800-30217000	Weak transcription	Right Ventricle	heart
23	chr15:30213800-30217200	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr15:30213800-30217200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:30214000-30216400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr15:30214000-30216400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr15:30214000-30216400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:30214000-30216600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr15:30214000-30216600	Enhancers	A549	lung
30	chr15:30214000-30216800	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr15:30214000-30216800	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:30214200-30216400	Weak transcription	Placenta	Placenta
33	chr15:30214200-30216600	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr15:30214400-30216400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr15:30214600-30216600	Weak transcription	HMEC	breast
36	chr15:30215000-30218600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:30215200-30217200	Enhancers	NHEK	skin
38	chr15:30215200-30218600	Enhancers	Fetal Heart	heart
39	chr15:30215600-30218200	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr15:30215800-30216800	Enhancers	NH-A	brain
41	chr15:30215800-30218600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr15:30216000-30216400	Enhancers	Brain Cingulate Gyrus	brain
43	chr15:30216000-30216800	Enhancers	Osteobl	bone
44	chr15:30216000-30218000	Enhancers	HSMMtube	muscle
45	chr15:30216000-30218200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:30216000-30218600	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr15:30216000-30218800	Enhancers	Fetal Intestine Large	intestine
48	chr15:30216200-30216600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:30216200-30216600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr15:30216200-30216600	Weak transcription	Placenta Amnion	Placenta Amnion

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