Variant report

Variant	rs28674681
Chromosome Location	chr15:51559917-51559918
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:51554656..51556788-chr15:51559710..51562112,2	MCF-7	breast:
2	chr15:51558883..51561621-chr17:57921193..57923679,2	MCF-7	breast:
3	chr15:51559197..51561555-chr15:51564918..51567091,2	K562	blood:

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10519299	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1062033	0.81[EUR][1000 genomes]
rs11632903	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11632926	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11636403	0.83[EUR][1000 genomes]
rs11636639	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12050767	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12901187	0.93[EUR][1000 genomes]
rs12907866	0.81[EUR][1000 genomes]
rs12908960	0.81[EUR][1000 genomes]
rs12910259	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17523527	0.99[EUR][1000 genomes]
rs17523541	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17601876	0.84[EUR][1000 genomes]
rs2414100	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2414101	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28440805	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28490942	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28518777	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28520437	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28637352	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2899474	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34712049	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34784350	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35939475	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3889391	0.95[EUR][1000 genomes]
rs4545755	0.89[EUR][1000 genomes]
rs4774584	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6493494	0.94[EUR][1000 genomes]
rs7181429	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs749292	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8028111	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8029537	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8038715	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8039089	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8042086	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[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	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	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
4	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	nsv904215	chr15:51542193-51673125	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51524800-51574000	Weak transcription	HepG2	liver
2	chr15:51558600-51560000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:51558600-51560200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:51558800-51560000	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:51558800-51560000	Active TSS	Brain Anterior Caudate	brain
6	chr15:51559000-51560000	Active TSS	Right Atrium	heart
7	chr15:51559000-51560200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:51559000-51560200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr15:51559000-51560200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr15:51559000-51560200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:51559000-51560200	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr15:51559000-51560200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
13	chr15:51559000-51560200	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
14	chr15:51559000-51560400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:51559000-51560400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
16	chr15:51559000-51560400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
17	chr15:51559200-51560000	Active TSS	Breast Myoepithelial Primary Cells	Breast
18	chr15:51559200-51560000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
19	chr15:51559200-51560000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr15:51559200-51560000	Active TSS	Brain Substantia Nigra	brain
21	chr15:51559200-51560000	Bivalent/Poised TSS	Colonic Mucosa	Colon
22	chr15:51559200-51560000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
23	chr15:51559200-51560000	Bivalent/Poised TSS	NHLF	lung
24	chr15:51559200-51560200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
25	chr15:51559200-51560200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr15:51559200-51560200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr15:51559200-51560200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr15:51559200-51560200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
29	chr15:51559200-51560200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
30	chr15:51559200-51560200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
31	chr15:51559200-51560200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:51559200-51560200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr15:51559200-51560200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
34	chr15:51559200-51560200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
35	chr15:51559200-51560200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr15:51559200-51560200	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr15:51559200-51560200	Flanking Active TSS	Liver	Liver
38	chr15:51559200-51560200	Active TSS	Brain Germinal Matrix	brain
39	chr15:51559200-51560200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
40	chr15:51559200-51560200	Active TSS	Fetal Kidney	kidney
41	chr15:51559200-51560200	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr15:51559200-51560200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
43	chr15:51559200-51560200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
44	chr15:51559200-51560200	Active TSS	NHDF-Ad	bronchial
45	chr15:51559200-51560200	Flanking Bivalent TSS/Enh	NHEK	skin
46	chr15:51559200-51560400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:51559200-51560400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:51559200-51560400	Active TSS	Aorta	Aorta
49	chr15:51559200-51560400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
50	chr15:51559400-51560000	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived

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