Variant report

Variant	rs71472440
Chromosome Location	chr15:40732793-40732794
allele	A/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	MXI1	chr15:40731395-40734925	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr15:40728064-40734370	K562	blood:	n/a	n/a
3	MAX	chr15:40732733-40733244	MCF-7	breast:	n/a	chr15:40732747-40732757 chr15:40732940-40732950
4	SIN3A	chr15:40731624-40734535	H1-hESC	embryonic stem cell:	n/a	chr15:40732000-40732008 chr15:40733072-40733085 chr15:40734006-40734017 chr15:40732439-40732450
5	NFYA	chr15:40732739-40733257	Hela-S3	cervix:	n/a	chr15:40733064-40733076 chr15:40732988-40733003 chr15:40733060-40733075 chr15:40733092-40733107 chr15:40732988-40733003 chr15:40732991-40733001 chr15:40733093-40733107 chr15:40732992-40733004 chr15:40733063-40733073 chr15:40733092-40733107 chr15:40732990-40733003 chr15:40733095-40733105 chr15:40732989-40733003 chr15:40733096-40733108 chr15:40733056-40733074
6	SP1	chr15:40732774-40733205	GM12878	blood:	n/a	chr15:40733049-40733060 chr15:40733085-40733106 chr15:40733051-40733060 chr15:40733049-40733061 chr15:40733049-40733061 chr15:40732902-40732912 chr15:40732903-40732912 chr15:40732901-40732913 chr15:40732981-40733002 chr15:40732901-40732913 chr15:40732902-40732916
7	MAX	chr15:40732769-40733117	K562	blood:	n/a	chr15:40732940-40732950
8	NFYA	chr15:40732746-40733201	GM12878	blood:	n/a	chr15:40733064-40733076 chr15:40732988-40733003 chr15:40733060-40733075 chr15:40733092-40733107 chr15:40732988-40733003 chr15:40732991-40733001 chr15:40733093-40733107 chr15:40732992-40733004 chr15:40733063-40733073 chr15:40733092-40733107 chr15:40732990-40733003 chr15:40733095-40733105 chr15:40732989-40733003 chr15:40733096-40733108 chr15:40733056-40733074
9	POLR2A	chr15:40731974-40733265	PFSK-1	brain:	n/a	n/a
10	POLR2A	chr15:40732698-40733695	NB4	blood:	n/a	n/a
11	MAX	chr15:40732660-40733587	A549	lung:	n/a	chr15:40732747-40732757 chr15:40732940-40732950
12	POLR2A	chr15:40732667-40733380	HepG2	liver:	n/a	n/a
13	POLR2A	chr15:40731312-40733266	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr15:40732379-40733269	H1-hESC	embryonic stem cell:	n/a	chr15:40732747-40732757 chr15:40732940-40732950
15	MAX	chr15:40732529-40733035	H1-hESC	embryonic stem cell:	n/a	chr15:40732747-40732757 chr15:40732940-40732950
16	MAX	chr15:40732687-40733259	HepG2	liver:	n/a	chr15:40732747-40732757 chr15:40732940-40732950
17	CHD2	chr15:40732757-40733786	Hela-S3	cervix:	n/a	chr15:40733663-40733673 chr15:40733500-40733510 chr15:40732935-40732945
18	TCF12	chr15:40731717-40733275	ECC-1	luminal epithelium:	n/a	chr15:40732643-40732653 chr15:40732011-40732018
19	NFYB	chr15:40732692-40733254	Hela-S3	cervix:	n/a	chr15:40733064-40733076 chr15:40733062-40733077 chr15:40732988-40733003 chr15:40733060-40733075 chr15:40733092-40733107 chr15:40733094-40733109 chr15:40732988-40733003 chr15:40732991-40733001 chr15:40733093-40733107 chr15:40732992-40733004 chr15:40733063-40733073 chr15:40733092-40733107 chr15:40732990-40733003 chr15:40733095-40733105 chr15:40732989-40733003 chr15:40733026-40733041 chr15:40733096-40733108
20	POLR2A	chr15:40732723-40733198	U87	brain:	n/a	n/a
21	POLR2A	chr15:40732691-40733640	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr15:40732677-40733763	H1-neurons	neurons:	n/a	n/a
23	POLR2A	chr15:40731422-40733782	K562	blood:	n/a	n/a
24	USF1	chr15:40732767-40733172	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr15:40732727-40733198	U87	brain:	n/a	n/a
26	EP300	chr15:40732752-40733133	K562	blood:	n/a	n/a
27	MYC	chr15:40731745-40733764	K562	blood:	n/a	chr15:40732747-40732757 chr15:40732940-40732950
28	SIN3AK20	chr15:40731647-40732901	H1-hESC	embryonic stem cell:	n/a	n/a
29	RCOR1	chr15:40731458-40733568	K562	blood:	n/a	n/a
30	RFX5	chr15:40731436-40734230	SK-N-SH	brain:	n/a	chr15:40733095-40733104 chr15:40732991-40733000 chr15:40732189-40732203
31	POLR2A	chr15:40730936-40733250	SK-N-MC	brain:	n/a	n/a
32	CCNT2	chr15:40732586-40734614	K562	blood:	n/a	chr15:40732903-40732912 chr15:40734332-40734341 chr15:40733476-40733485
33	E2F6	chr15:40732738-40733223	H1-hESC	embryonic stem cell:	n/a	chr15:40733096-40733105 chr15:40733064-40733073
34	POLR2A	chr15:40730497-40732956	K562	blood:	n/a	n/a
35	POLR2A	chr15:40732773-40733769	GM18951	blood:	n/a	n/a
36	ELF1	chr15:40732548-40733227	GM12878	blood:	n/a	chr15:40733188-40733200
37	ELF1	chr15:40732792-40733371	MCF-7	breast:	n/a	chr15:40733188-40733200
38	SP1	chr15:40732742-40733273	A549	lung:	n/a	chr15:40733049-40733060 chr15:40733085-40733106 chr15:40733051-40733060 chr15:40733049-40733061 chr15:40733049-40733061 chr15:40732902-40732912 chr15:40732903-40732912 chr15:40732901-40732913 chr15:40732981-40733002 chr15:40732901-40732913 chr15:40732902-40732916
39	NFYB	chr15:40732692-40733309	GM12878	blood:	n/a	chr15:40733064-40733076 chr15:40733062-40733077 chr15:40732988-40733003 chr15:40733060-40733075 chr15:40733092-40733107 chr15:40733094-40733109 chr15:40732988-40733003 chr15:40732991-40733001 chr15:40733093-40733107 chr15:40732992-40733004 chr15:40733063-40733073 chr15:40733092-40733107 chr15:40732990-40733003 chr15:40733095-40733105 chr15:40732989-40733003 chr15:40733026-40733041 chr15:40733096-40733108
40	POLR2A	chr15:40731546-40733944	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr15:40732749-40733219	K562	blood:	n/a	n/a
42	SIN3AK20	chr15:40732739-40734587	PANC-1	pancreas:	n/a	n/a
43	NFYA	chr15:40732548-40733263	K562	blood:	n/a	chr15:40733064-40733076 chr15:40732988-40733003 chr15:40733060-40733075 chr15:40733092-40733107 chr15:40732988-40733003 chr15:40732991-40733001 chr15:40733093-40733107 chr15:40732992-40733004 chr15:40733063-40733073 chr15:40733092-40733107 chr15:40732990-40733003 chr15:40733095-40733105 chr15:40732989-40733003 chr15:40733096-40733108 chr15:40733056-40733074
44	HCFC1	chr15:40732765-40733691	Hela-S3	cervix:	n/a	n/a
45	MYC	chr15:40732647-40733041	K562	blood:	n/a	chr15:40732747-40732757 chr15:40732940-40732950
46	ELF1	chr15:40732388-40733681	GM12878	blood:	n/a	chr15:40733188-40733200 chr15:40732421-40732432
47	IRF1	chr15:40732782-40733162	K562	blood:	n/a	chr15:40733096-40733105
48	POLR2A	chr15:40731670-40733548	K562	blood:	n/a	n/a
49	MAX	chr15:40732415-40733305	ECC-1	luminal epithelium:	n/a	chr15:40732747-40732757 chr15:40732940-40732950
50	POLR2A	chr15:40731597-40733761	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40731663..40736686-chr15:40795056..40800792,8	K562	blood:
2	chr12:52444658..52445325-chr15:40732483..40733451,2	Hela-S3	cervix:
3	chr15:40732401..40734895-chr15:40758444..40760752,2	K562	blood:
4	chr15:40731823..40734826-chr15:40760868..40766207,7	K562	blood:
5	chr15:40729975..40738939-chr15:40745780..40750666,13	K562	blood:
6	chr15:40659428..40662346-chr15:40732080..40734388,2	MCF-7	breast:
7	chr15:40731340..40734041-chr15:41045866..41047695,2	K562	blood:
8	chr12:120730578..120731103-chr15:40732693..40733606,2	Hela-S3	cervix:
9	chr15:40732257..40736129-chr15:40757677..40760458,4	MCF-7	breast:
10	chr15:40731621..40739951-chr15:40753297..40765462,23	K562	blood:
11	chr15:40730539..40734458-chr15:40797952..40800684,3	K562	blood:
12	chr15:40731794..40734704-chr15:40761511..40763222,2	MCF-7	breast:

Variant related genes	Relation type
BAHD1	TF binding region
ENSG00000140323	Chromatin interaction
ENSG00000169105	Chromatin interaction
ENSG00000123358	Chromatin interaction
ENSG00000140320	Chromatin interaction
ENSG00000259211	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000259368	Chromatin interaction
ENSG00000259364	Chromatin interaction
ENSG00000259536	Chromatin interaction
ENSG00000137824	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11853333	0.84[EUR][1000 genomes]
rs12898690	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	esv3442593	chr15:40731460-40735058	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
3	esv3437607	chr15:40732210-40735158	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	esv3377736	chr15:40732285-40734833	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs71472440	C15orf57	cis	Esophagus Muscularis	GTEx
rs71472440	RP11-111A22.1	cis	lung	GTEx
rs71472440	C15orf57	cis	Adipose Subcutaneous	GTEx
rs71472440	C15orf57	cis	lung	GTEx
rs71472440	RP11-111A22.1	cis	Artery Tibial	GTEx
rs71472440	C15orf57	cis	Esophagus Mucosa	GTEx
rs71472440	C15orf57	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40731200-40732800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
2	chr15:40731200-40734800	Active TSS	H9 Cell Line	embryonic stem cell
3	chr15:40731400-40732800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr15:40731400-40736000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:40731600-40732800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:40731600-40732800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:40731600-40732800	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
8	chr15:40731600-40734800	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr15:40731600-40735000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:40731600-40735200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr15:40731800-40732800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr15:40731800-40732800	Flanking Active TSS	Adipose Nuclei	Adipose
13	chr15:40731800-40732800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
14	chr15:40731800-40732800	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
15	chr15:40731800-40732800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
16	chr15:40731800-40732800	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
17	chr15:40731800-40732800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
18	chr15:40731800-40732800	Flanking Bivalent TSS/Enh	Dnd41	blood
19	chr15:40731800-40732800	Flanking Active TSS	HMEC	breast
20	chr15:40731800-40732800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
21	chr15:40731800-40733400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:40731800-40734800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:40731800-40734800	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr15:40731800-40735000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
25	chr15:40731800-40735000	Active TSS	H1 Cell Line	embryonic stem cell
26	chr15:40731800-40735000	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr15:40731800-40735000	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr15:40731800-40735200	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr15:40732000-40732800	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:40732000-40732800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:40732000-40732800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
32	chr15:40732000-40732800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
33	chr15:40732000-40732800	Flanking Active TSS	Primary hematopoietic stem cells	blood
34	chr15:40732000-40732800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr15:40732000-40732800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
36	chr15:40732000-40732800	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
37	chr15:40732000-40732800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:40732000-40732800	Flanking Active TSS	Liver	Liver
39	chr15:40732000-40732800	Flanking Active TSS	Colonic Mucosa	Colon
40	chr15:40732000-40732800	Flanking Active TSS	Fetal Heart	heart
41	chr15:40732000-40732800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
42	chr15:40732000-40732800	Flanking Bivalent TSS/Enh	Thymus	Thymus
43	chr15:40732000-40732800	Flanking Active TSS	NHEK	skin
44	chr15:40732000-40733000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr15:40732000-40733000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
46	chr15:40732000-40733600	Active TSS	Right Atrium	heart
47	chr15:40732000-40734600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:40732000-40734600	Active TSS	A549	lung
49	chr15:40732000-40734800	Active TSS	K562	blood
50	chr15:40732000-40735400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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