Variant report

Variant	rs12908645
Chromosome Location	chr15:58845961-58845962
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:58812575..58815325-chr15:58843755..58846624,5	K562	blood:
2	chr15:58838998..58841145-chr15:58842509..58846691,3	MCF-7	breast:
3	chr15:58836656..58842196-chr15:58843431..58849915,8	K562	blood:
4	chr15:58812575..58816304-chr15:58843755..58846624,5	K562	blood:

Variant related genes	Relation type
ENSG00000259476	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs12913969	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17301857	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17301864	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2242063	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2242066	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28427123	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28458188	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28515698	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28524122	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28569241	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28602186	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36017602	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6074	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62005260	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs871804	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv569598	chr15:58552606-58852463	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3362898	chr15:58705732-58850860	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1043041	chr15:58744505-58876327	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv569601	chr15:58800766-58866156	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58829000-58847600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:58837000-58848400	Enhancers	Fetal Thymus	thymus
3	chr15:58840600-58849200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:58840800-58849600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr15:58842600-58846200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:58843200-58846200	Enhancers	Thymus	Thymus
7	chr15:58843400-58846400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr15:58844400-58847200	Weak transcription	GM12878-XiMat	blood
9	chr15:58844600-58846600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr15:58844600-58847000	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr15:58844600-58847000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr15:58844600-58847200	Weak transcription	Fetal Kidney	kidney
13	chr15:58844600-58848000	Weak transcription	A549	lung
14	chr15:58844600-58860400	Weak transcription	Primary T cells from cord blood	blood
15	chr15:58844800-58847200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:58844800-58847200	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:58844800-58850800	Weak transcription	Liver	Liver
18	chr15:58845000-58846600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr15:58845000-58847000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:58845000-58847400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:58845000-58847400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:58845000-58847400	Weak transcription	Brain Anterior Caudate	brain
23	chr15:58845000-58847400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:58845000-58847600	Weak transcription	Fetal Heart	heart
25	chr15:58845000-58847800	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:58845000-58848000	Weak transcription	Right Atrium	heart
27	chr15:58845200-58847400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:58845200-58847600	Weak transcription	Fetal Intestine Large	intestine
29	chr15:58845200-58847600	Weak transcription	Fetal Intestine Small	intestine
30	chr15:58845200-58847800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr15:58845200-58847800	Weak transcription	Small Intestine	intestine
32	chr15:58845200-58848000	Weak transcription	Colonic Mucosa	Colon
33	chr15:58845400-58847400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr15:58845400-58847400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:58845400-58847800	Weak transcription	Ovary	ovary
36	chr15:58845400-58857200	Weak transcription	Adipose Nuclei	Adipose
37	chr15:58845600-58847000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:58845600-58847400	Weak transcription	K562	blood
39	chr15:58845600-58847800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:58845600-58847800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr15:58845800-58847200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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