Variant report

Variant	rs12913423
Chromosome Location	chr15:56283960-56283961
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:56281891..56284127-chr15:56288031..56290159,2	K562	blood:
2	chr15:56283238..56284535-chr15:56344426..56345460,6	MCF-7	breast:
3	chr15:56282892..56284804-chr15:56387312..56388901,2	MCF-7	breast:
4	chr15:56282101..56284524-chr15:56536077..56539290,3	MCF-7	breast:
5	chr15:56282050..56287467-chr15:56534024..56538662,8	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151575	Chromatin interaction
ENSG00000181827	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1112535	0.92[ASN][1000 genomes]
rs12441706	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12911653	0.92[ASN][1000 genomes]
rs12911833	0.86[ASN][1000 genomes]
rs12913147	0.88[ASN][1000 genomes]
rs12915953	0.92[ASN][1000 genomes]
rs16976674	0.92[ASN][1000 genomes]
rs2036738	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2036740	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34077395	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34330530	0.92[ASN][1000 genomes]
rs34841076	0.92[ASN][1000 genomes]
rs35301686	0.90[ASN][1000 genomes]
rs35460567	0.87[ASN][1000 genomes]
rs35662811	0.92[ASN][1000 genomes]
rs35710039	0.91[ASN][1000 genomes]
rs35836088	0.92[ASN][1000 genomes]
rs35911067	0.92[ASN][1000 genomes]
rs35967908	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62046376	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71476762	0.87[ASN][1000 genomes]
rs71476763	0.92[ASN][1000 genomes]
rs71476768	0.92[ASN][1000 genomes]
rs7161742	0.91[ASN][1000 genomes]
rs7179929	0.92[ASN][1000 genomes]
rs9652429	0.94[AMR][1000 genomes];0.95[EUR][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	esv2761872	chr15:56211065-56426501	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv904245	chr15:56229760-56324451	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv457159	chr15:56255774-56321854	Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv569543	chr15:56255774-56321854	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv457160	chr15:56273446-56320235	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
6	nsv569544	chr15:56273446-56320235	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
7	nsv457161	chr15:56274443-56324451	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers 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	17 gene(s)	inside rSNPs	n/a
8	nsv569545	chr15:56274443-56324451	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a
9	nsv569546	chr15:56274443-56337527	Active TSS Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56231400-56284200	Weak transcription	Stomach Smooth Muscle	stomach
2	chr15:56248200-56285200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:56272600-56284200	Weak transcription	Lung	lung
4	chr15:56274400-56284000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:56275600-56284000	Weak transcription	Aorta	Aorta
6	chr15:56275600-56284200	Weak transcription	Left Ventricle	heart
7	chr15:56276400-56285000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:56276600-56284000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr15:56277200-56284200	Weak transcription	Fetal Muscle Trunk	muscle
10	chr15:56280200-56284000	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:56280400-56285200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr15:56281800-56284200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr15:56282200-56284600	Weak transcription	Fetal Stomach	stomach
14	chr15:56282400-56284200	Weak transcription	Psoas Muscle	Psoas
15	chr15:56282800-56284000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:56282800-56284200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:56282800-56284200	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr15:56282800-56284200	Enhancers	HepG2	liver
19	chr15:56282800-56284400	Enhancers	Fetal Muscle Leg	muscle
20	chr15:56282800-56284600	Enhancers	Small Intestine	intestine
21	chr15:56283000-56284000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr15:56283000-56284200	Enhancers	Primary neutrophils fromperipheralblood	blood
23	chr15:56283000-56284200	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr15:56283000-56284200	Enhancers	Colon Smooth Muscle	Colon
25	chr15:56283000-56284200	Enhancers	HSMMtube	muscle
26	chr15:56283000-56284600	Weak transcription	Fetal Kidney	kidney
27	chr15:56283000-56284800	Enhancers	Brain Substantia Nigra	brain
28	chr15:56283200-56285000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:56283400-56284200	Enhancers	Fetal Lung	lung
30	chr15:56283400-56284400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:56283400-56284600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:56283400-56284600	Flanking Active TSS	A549	lung
33	chr15:56283400-56285000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr15:56283600-56284000	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr15:56283600-56284000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
36	chr15:56283600-56284000	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr15:56283600-56284000	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr15:56283600-56284000	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr15:56283600-56284000	Active TSS	Skeletal Muscle Female	skeletal muscle
40	chr15:56283600-56284000	Enhancers	Stomach Mucosa	stomach
41	chr15:56283600-56284200	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr15:56283600-56284200	Enhancers	Adipose Nuclei	Adipose
43	chr15:56283600-56284200	Enhancers	Fetal Intestine Large	intestine
44	chr15:56283600-56284200	Enhancers	HMEC	breast
45	chr15:56283600-56284400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr15:56283600-56284400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:56283600-56284400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
48	chr15:56283600-56284400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:56283600-56284400	Transcr. at gene 5' and 3'	NHEK	skin
50	chr15:56283600-56284800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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