Variant report

Variant	rs58312028
Chromosome Location	chr15:40074345-40074346
allele	C/G
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	chr15:40074271-40075557	PFSK-1	brain:	n/a	n/a
2	MXI1	chr15:40074115-40077221	SK-N-SH	brain:	n/a	chr15:40075015-40075030 chr15:40075017-40075032
3	POLR2A	chr15:40074290-40076223	PBDE	blood:	n/a	n/a
4	PML	chr15:40074317-40075516	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:40074342-40076610	HUVEC	blood vessel:	n/a	n/a
6	HCFC1	chr15:40074147-40076109	Hela-S3	cervix:	n/a	n/a
7	MAFK	chr15:40074141-40074428	K562	blood:	n/a	n/a
8	MAFF	chr15:40074146-40074392	HepG2	liver:	n/a	chr15:40074241-40074259
9	STAT3	chr15:40074303-40074503	MCF10A-Er-Src	breast:	n/a	n/a
10	WRNIP1	chr15:40074311-40074497	GM12878	blood:	n/a	n/a
11	BACH1	chr15:40074236-40074539	K562	blood:	n/a	n/a
12	CUX1	chr15:40074293-40074573	K562	blood:	n/a	n/a
13	NFYB	chr15:40074326-40075207	GM12878	blood:	n/a	chr15:40074696-40074711 chr15:40074697-40074711 chr15:40074696-40074711
14	IRF1	chr15:40074310-40075421	K562	blood:	n/a	chr15:40074755-40074769 chr15:40074760-40074774 chr15:40074686-40074700 chr15:40074665-40074679
15	POLR2A	chr15:40074292-40075445	U87	brain:	n/a	n/a
16	MAFF	chr15:40074212-40074517	K562	blood:	n/a	chr15:40074241-40074259
17	POLR2A	chr15:40074286-40075445	U87	brain:	n/a	n/a
18	POLR2A	chr15:40074283-40074719	U87	brain:	n/a	n/a
19	MAFK	chr15:40074085-40074531	HepG2	liver:	n/a	n/a
20	POLR2A	chr15:40074331-40076370	SK-N-SH	brain:	n/a	n/a
21	POLR2A	chr15:40074270-40074719	U87	brain:	n/a	n/a
22	JUND	chr15:40074167-40076856	SK-N-SH	brain:	n/a	chr15:40074698-40074707
23	POLR2A	chr15:40074311-40075449	PFSK-1	brain:	n/a	n/a
24	REST	chr15:40074173-40075999	H1-neurons	neurons:	n/a	chr15:40074763-40074776 chr15:40075089-40075102 chr15:40074705-40074714

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40069274..40072171-chr15:40072532..40074529,2	MCF-7	breast:
2	chr15:40074208..40076102-chr15:40329673..40331654,2	K562	blood:

Variant related genes	Relation type
ENSG00000261136	TF binding region
ENSG00000140319	Chromatin interaction
ENSG00000248508	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1027232	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858148	0.81[ASN][1000 genomes]
rs12437837	0.81[ASN][1000 genomes]
rs12440567	0.85[ASN][1000 genomes]
rs2171312	0.85[ASN][1000 genomes]
rs2631717	0.82[ASN][1000 genomes]
rs28538495	0.85[ASN][1000 genomes]
rs28884199	0.85[ASN][1000 genomes]
rs28896916	0.85[ASN][1000 genomes]
rs4924387	0.81[ASN][1000 genomes]
rs4924388	0.85[ASN][1000 genomes]
rs4924392	0.90[ASN][1000 genomes]
rs59434895	0.81[ASN][1000 genomes]
rs60431166	0.81[ASN][1000 genomes]
rs61695850	0.81[ASN][1000 genomes]
rs6492915	0.82[EUR][1000 genomes]
rs7165244	0.91[EUR][1000 genomes]
rs73397133	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026892	0.94[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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40059400-40074400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:40070200-40074400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:40070400-40074400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:40070600-40074400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:40073800-40074400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr15:40073800-40074400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr15:40073800-40074600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:40073800-40074600	Flanking Active TSS	Dnd41	blood
9	chr15:40073800-40075400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:40073800-40075600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:40074000-40074400	Flanking Active TSS	K562	blood
12	chr15:40074000-40074600	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr15:40074000-40074600	Flanking Active TSS	Primary T cells from cord blood	blood
14	chr15:40074000-40074600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:40074000-40074600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr15:40074000-40074600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr15:40074000-40075400	Active TSS	Liver	Liver
18	chr15:40074000-40075400	Active TSS	Rectal Smooth Muscle	rectum
19	chr15:40074000-40075600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:40074000-40075600	Active TSS	Brain Angular Gyrus	brain
21	chr15:40074000-40075600	Active TSS	Rectal Mucosa Donor 29	rectum
22	chr15:40074000-40075800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:40074000-40075800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:40074000-40076400	Active TSS	A549	lung
25	chr15:40074000-40076600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:40074200-40074400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
27	chr15:40074200-40074400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr15:40074200-40074400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr15:40074200-40074400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
30	chr15:40074200-40074400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:40074200-40074400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr15:40074200-40074400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr15:40074200-40074400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:40074200-40074400	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr15:40074200-40074400	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr15:40074200-40074400	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr15:40074200-40074400	Enhancers	Fetal Heart	heart
38	chr15:40074200-40074400	Flanking Active TSS	Fetal Lung	lung
39	chr15:40074200-40074400	Enhancers	Fetal Thymus	thymus
40	chr15:40074200-40074400	Flanking Active TSS	HepG2	liver
41	chr15:40074200-40074400	Enhancers	HMEC	breast
42	chr15:40074200-40074400	Flanking Active TSS	NHDF-Ad	bronchial
43	chr15:40074200-40074600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr15:40074200-40074600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
45	chr15:40074200-40074600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
46	chr15:40074200-40074600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr15:40074200-40074600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr15:40074200-40074600	Flanking Active TSS	Primary B cells from peripheral blood	blood
49	chr15:40074200-40074600	Flanking Active TSS	Primary hematopoietic stem cells	blood
50	chr15:40074200-40074600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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