Variant report

Variant	rs7173137
Chromosome Location	chr15:57026346-57026347
allele	A/C
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	TCF12	chr15:57025369-57026455	MCF-7	breast:	n/a	n/a
2	E2F6	chr15:57024807-57026861	H1-hESC	embryonic stem cell:	n/a	chr15:57025488-57025498 chr15:57025541-57025550 chr15:57025808-57025818 chr15:57025866-57025881
3	TEAD4	chr15:57025632-57026376	K562	blood:	n/a	n/a
4	MYC	chr15:57024000-57026500	A549	lung:	n/a	chr15:57025943-57025952
5	GTF2F1	chr15:57024991-57026680	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAFK	chr15:57026200-57026451	HepG2	liver:	n/a	n/a
7	E2F6	chr15:57024968-57026543	A549	lung:	n/a	chr15:57025488-57025498 chr15:57025541-57025550 chr15:57025808-57025818 chr15:57025866-57025881
8	MXI1	chr15:57024763-57026365	IMR90	lung:	n/a	n/a
9	MAZ	chr15:57024775-57026474	IMR90	lung:	n/a	chr15:57025943-57025952
10	CBX3	chr15:57025036-57026468	HCT-116	colon:	n/a	n/a
11	POLR2A	chr15:57024730-57026664	MCF10A-Er-Src	breast:	n/a	n/a
12	KAP1	chr15:57025728-57027111	HEK293	kidney:	n/a	n/a
13	SETDB1	chr15:57025688-57027009	U2OS	brain:	n/a	n/a
14	KAP1	chr15:57025863-57026730	K562	blood:	n/a	n/a
15	JUN	chr15:57023652-57026813	K562	blood:	n/a	chr15:57025885-57025894 chr15:57026028-57026042
16	TCF12	chr15:57024702-57026727	A549	lung:	n/a	n/a
17	MAX	chr15:57024978-57026394	HCT-116	colon:	n/a	chr15:57025943-57025952
18	MAX	chr15:57025048-57026394	A549	lung:	n/a	chr15:57025943-57025952
19	MAX	chr15:57024974-57026375	ECC-1	luminal epithelium:	n/a	chr15:57025943-57025952
20	MAFK	chr15:57026214-57026410	HepG2	liver:	n/a	n/a
21	REST	chr15:57024819-57026426	A549	lung:	n/a	chr15:57025608-57025621 chr15:57025368-57025381
22	MAX	chr15:57025003-57026448	K562	blood:	n/a	chr15:57025943-57025952
23	MAFF	chr15:57026290-57026389	K562	blood:	n/a	n/a
24	MAX	chr15:57024987-57026385	H1-hESC	embryonic stem cell:	n/a	chr15:57025943-57025952
25	BCL3	chr15:57025652-57026449	A549	lung:	n/a	chr15:57026115-57026124
26	MAFF	chr15:57026216-57026427	HepG2	liver:	n/a	n/a
27	TEAD4	chr15:57025645-57026356	K562	blood:	n/a	n/a
28	TBL1XR1	chr15:57025248-57026603	K562	blood:	n/a	n/a
29	E2F6	chr15:57025077-57026368	K562	blood:	n/a	chr15:57025488-57025498 chr15:57025541-57025550 chr15:57025808-57025818 chr15:57025866-57025881
30	RCOR1	chr15:57024268-57026356	IMR90	lung:	n/a	n/a
31	MAX	chr15:57024582-57026582	A549	lung:	n/a	chr15:57025943-57025952
32	MAX	chr15:57024724-57026480	A549	lung:	n/a	chr15:57025943-57025952
33	E2F6	chr15:57024999-57026450	H1-hESC	embryonic stem cell:	n/a	chr15:57025488-57025498 chr15:57025541-57025550 chr15:57025808-57025818 chr15:57025866-57025881

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:57026315-57026365	PrEC	prostate:	n/a
2	chr15:57026315-57026365	ovcar-3	ovarian:	n/a
3	chr15:57026315-57026365	RPTEC	kidney:	n/a
4	chr15:57026315-57026365	HAEpiC	amniotic membrane:	n/a
5	chr15:57026315-57026365	NH-A	brain:	n/a
6	chr15:57026315-57026365	NHBE	bronchial:	n/a
7	chr15:57026315-57026365	AoSMC	blood vessel:	n/a
8	chr15:57026315-57026365	SK-N-SH_RA	brain:	n/a
9	chr15:57026315-57026365	HepG2	liver:	n/a
10	chr15:57026315-57026365	SK-N-MC	brain:	n/a
11	chr15:57026315-57026365	NT2-D1	testis:	n/a
12	chr15:57026315-57026365	A549	lung:	n/a
13	chr15:57026315-57026365	Caco-2	colon:	n/a
14	chr15:57026315-57026365	GM19239	blood:	n/a
15	chr15:57026315-57026365	GM12892	blood:	n/a
16	chr15:57026315-57026365	MCF10A-Er-Src	breast:	n/a
17	chr15:57026315-57026365	HEK293	kidney:	embryo
18	chr15:57026315-57026365	SK-N-SH	brain:	n/a
19	chr15:57026315-57026365	NHDF-neo	bronchial:	n/a
20	chr15:57026315-57026365	GM12878	blood:	n/a
21	chr15:57026315-57026365	CMK	blood:	n/a
22	chr15:57026315-57026365	HNPCEpiC	eye:	n/a
23	chr15:57026315-57026365	PFSK-1	brain:	n/a
24	chr15:57026315-57026365	HCT-116	colon:	n/a
25	chr15:57026315-57026365	Jurkat	blood:	n/a
26	chr15:57026315-57026365	K562	blood:	n/a
27	chr15:57026315-57026365	HEEpiC	esophagus:	n/a
28	chr15:57026315-57026365	LNCaP	prostate:	n/a
29	chr15:57026315-57026365	AG04450	lung:	fetal
30	chr15:57026315-57026365	ProgFib	skin:	n/a
31	chr15:57026315-57026365	HRPEpiC	eye:	n/a
32	chr15:57026315-57026365	AG09309	skin:	n/a
33	chr15:57026315-57026365	AG04449	skin:	fetal
34	chr15:57026315-57026365	H1-hESC	embryonic stem cell:	embryo
35	chr15:57026315-57026365	AG10803	skin:	n/a
36	chr15:57026315-57026365	SAEC	small airway:	n/a
37	chr15:57026315-57026365	AG09319	gingival:	n/a
38	chr15:57026315-57026365	HPAEpiC	pulmonary alveolar:	n/a
39	chr15:57026315-57026365	GM06990	blood:	n/a
40	chr15:57026315-57026365	SKMC	muscle:	n/a
41	chr15:57026315-57026365	HIPEpiC	eye:	n/a
42	chr15:57026315-57026365	Hepatocyte	liver:	n/a
43	chr15:57026315-57026365	HUVEC	blood vessel:	n/a
44	chr15:57026315-57026365	HCPEpiC	choroid plexus:	n/a
45	chr15:57026315-57026365	HL-60	blood:	n/a
46	chr15:57026315-57026365	BE2_C	brain:	n/a
47	chr15:57026315-57026365	HCM	heart:	n/a
48	chr15:57026315-57026365	ECC-1	luminal epithelium:	n/a
49	chr15:57026315-57026365	U87	brain:	n/a
50	chr15:57026315-57026365	MCF-7	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:57023111..57027218-chr15:57209095..57213054,4	K562	blood:
2	chr15:56534684..56537162-chr15:57025486..57027553,2	MCF-7	breast:
3	chr15:57022824..57027100-chr15:57611258..57614634,3	K562	blood:
4	chr1:149223243..149225441-chr15:57024407..57026352,2	MCF-7	breast:
5	chr15:56997588..56999927-chr15:57024317..57027282,2	K562	blood:
6	chr15:57023339..57026885-chr15:57210242..57212303,3	MCF-7	breast:

Variant related genes	Relation type
ZNF280D	TF binding region
ZNF280D	CpG island
ENSG00000151575	Chromatin interaction
ENSG00000140262	Chromatin interaction
ENSG00000260172	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000181827	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10518871	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10518878	0.84[EUR][1000 genomes]
rs11071290	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11852822	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11856432	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2128171	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28437201	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6493882	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6493886	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6493892	0.86[EUR][1000 genomes]
rs7164095	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7166876	0.86[EUR][1000 genomes]
rs7171500	0.85[ASN][1000 genomes]
rs7178196	0.85[EUR][1000 genomes]
rs7182691	0.84[EUR][1000 genomes]
rs9919955	0.81[EUR][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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv569576	chr15:57012816-57126917	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv3449418	chr15:57024810-57026908	Active TSS Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7173137	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57024200-57026400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:57024400-57026400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr15:57024600-57026400	Active TSS	Brain Anterior Caudate	brain
4	chr15:57024600-57026400	Active TSS	Brain Substantia Nigra	brain
5	chr15:57024800-57026400	Active TSS	Liver	Liver
6	chr15:57024800-57026400	Active TSS	Brain Angular Gyrus	brain
7	chr15:57024800-57026400	Active TSS	Brain Inferior Temporal Lobe	brain
8	chr15:57024800-57026400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr15:57024800-57026400	Active TSS	Fetal Brain Female	brain
10	chr15:57024800-57026400	Active TSS	Fetal Kidney	kidney
11	chr15:57024800-57026400	Active TSS	Fetal Lung	lung
12	chr15:57024800-57026400	Active TSS	HSMMtube	muscle
13	chr15:57024800-57026800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr15:57025200-57026400	Active TSS	Primary T cells from cord blood	blood
15	chr15:57025400-57026400	Active TSS	Primary B cells from cord blood	blood
16	chr15:57025600-57026400	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr15:57025800-57026400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
18	chr15:57025800-57026400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr15:57025800-57026400	Flanking Active TSS	Thymus	Thymus
20	chr15:57025800-57026400	Flanking Active TSS	Dnd41	blood
21	chr15:57025800-57026400	Flanking Active TSS	Hela-S3	cervix
22	chr15:57025800-57026400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr15:57026000-57026400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
24	chr15:57026000-57026400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:57026000-57026400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
26	chr15:57026000-57026400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
27	chr15:57026000-57026400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
28	chr15:57026000-57026400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:57026000-57026400	Flanking Active TSS	Fetal Brain Male	brain
30	chr15:57026000-57026400	Flanking Active TSS	Placenta	Placenta
31	chr15:57026000-57026400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
32	chr15:57026000-57026400	Enhancers	Stomach Mucosa	stomach
33	chr15:57026000-57026400	Enhancers	HepG2	liver
34	chr15:57026000-57026400	Flanking Active TSS	K562	blood
35	chr15:57026000-57026600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr15:57026000-57026800	ZNF genes & repeats	Fetal Thymus	thymus
37	chr15:57026000-57027200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
38	chr15:57026000-57028600	Weak transcription	HUVEC	blood vessel
39	chr15:57026000-57029400	Weak transcription	NH-A	brain
40	chr15:57026200-57026400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
41	chr15:57026200-57026400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr15:57026200-57026400	Enhancers	Primary T cells fromperipheralblood	blood
43	chr15:57026200-57026400	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr15:57026200-57026400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
45	chr15:57026200-57026400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr15:57026200-57026400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr15:57026200-57026400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:57026200-57026400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr15:57026200-57026400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:57026200-57026400	Flanking Active TSS	Brain Cingulate Gyrus	brain

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