Variant report

Variant	rs592172
Chromosome Location	chr15:40079390-40079391
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:40079383-40079451	A549	lung:	n/a	n/a
2	SMC3	chr15:40078439-40079486	SK-N-SH	brain:	n/a	chr15:40078869-40078883
3	RAD21	chr15:40078461-40079761	SK-N-SH	brain:	n/a	chr15:40078868-40078887 chr15:40078870-40078877
4	POLR2A	chr15:40079369-40079486	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr15:40078471-40079523	A549	lung:	n/a	chr15:40078872-40078880 chr15:40078867-40078885 chr15:40078869-40078890 chr15:40078868-40078884 chr15:40078870-40078883

No.	Distal block	Cell Line	Cell type
1	chr15:39877336..39879438-chr15:40075503..40079395,4	MCF-7	breast:
2	chr15:40078363..40080929-chr15:40268662..40270401,2	MCF-7	breast:
3	chr15:40076890..40079993-chr15:40222713..40226528,3	K562	blood:
4	chr15:40074604..40078535-chr15:40078976..40081815,4	K562	blood:
5	chr15:39873007..39875919-chr15:40078387..40080697,2	MCF-7	breast:
6	chr15:40074241..40077863-chr15:40078792..40081577,3	K562	blood:
7	chr15:40078993..40080916-chr15:40082332..40084803,2	K562	blood:
8	chr15:40078779..40080616-chr15:40094906..40097630,2	MCF-7	breast:
9	chr15:40078638..40079472-chr15:40566591..40567310,2	MCF-7	breast:
10	chr15:40051644..40053868-chr15:40078451..40080226,2	MCF-7	breast:
11	chr15:40079175..40081149-chr15:40487705..40489916,2	K562	blood:

Variant related genes	Relation type
FSIP1	TF binding region
ENSG00000150667	Chromatin interaction
ENSG00000128829	Chromatin interaction
ENSG00000261136	Chromatin interaction
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1166718	0.93[ASN][1000 genomes]
rs1166722	0.95[ASN][1000 genomes]
rs1166723	0.94[ASN][1000 genomes]
rs12592687	0.90[ASN][1000 genomes]
rs1688087	0.95[ASN][1000 genomes]
rs2576929	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2576932	0.93[ASN][1000 genomes]
rs2576933	0.93[ASN][1000 genomes]
rs2631714	0.94[ASN][1000 genomes]
rs2638009	0.92[ASN][1000 genomes]
rs34943556	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4115216	0.86[ASN][1000 genomes]
rs4924389	0.95[ASN][1000 genomes]
rs4924391	0.95[ASN][1000 genomes]
rs594863	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs606927	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs620407	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6492914	0.83[ASN][1000 genomes]
rs6492919	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66496275	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs670748	0.92[ASN][1000 genomes]
rs7165244	0.86[ASN][1000 genomes]
rs7179417	0.87[ASN][1000 genomes]
rs8031241	0.85[ASN][1000 genomes]
rs8033485	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40075800-40079400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr15:40075800-40080600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:40076000-40079600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr15:40076000-40080600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr15:40076000-40081000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:40076000-40103200	Weak transcription	Right Atrium	heart
7	chr15:40076200-40079800	Weak transcription	Pancreas	Pancrea
8	chr15:40076200-40080000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:40076200-40080800	Weak transcription	Primary B cells from cord blood	blood
10	chr15:40076200-40081400	Weak transcription	Fetal Kidney	kidney
11	chr15:40076400-40080600	Weak transcription	Thymus	Thymus
12	chr15:40076600-40079400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:40076600-40079800	Weak transcription	Fetal Thymus	thymus
14	chr15:40076600-40080000	Enhancers	HMEC	breast
15	chr15:40076600-40080200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:40076600-40080600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:40076600-40080600	Weak transcription	Duodenum Mucosa	Duodenum
18	chr15:40076600-40081600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr15:40076600-40082000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr15:40076600-40082400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:40076600-40082600	Weak transcription	Primary T cells from cord blood	blood
22	chr15:40076600-40084200	Weak transcription	Adipose Nuclei	Adipose
23	chr15:40076600-40086200	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:40076600-40090200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:40076600-40092600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr15:40076800-40082200	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr15:40076800-40082400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr15:40077200-40079800	Weak transcription	HSMMtube	muscle
29	chr15:40077200-40081200	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr15:40077200-40082600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:40077200-40082600	Enhancers	NHLF	lung
32	chr15:40077200-40092600	Weak transcription	NHEK	skin
33	chr15:40077200-40093200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:40077400-40082600	Enhancers	Osteobl	bone
35	chr15:40077600-40079800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:40077600-40082400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr15:40077600-40094600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr15:40077800-40079600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr15:40077800-40080000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:40077800-40081200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr15:40077800-40082600	Enhancers	HUES64 Cell Line	embryonic stem cell
42	chr15:40078000-40079600	Weak transcription	Fetal Lung	lung
43	chr15:40078000-40080600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr15:40078000-40082000	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr15:40078200-40081200	Enhancers	HSMM	muscle
46	chr15:40078200-40081400	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr15:40078200-40082400	Enhancers	Muscle Satellite Cultured Cells	--
48	chr15:40078400-40079400	Enhancers	Fetal Heart	heart
49	chr15:40078600-40079400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr15:40078600-40079600	Enhancers	Liver	Liver

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