Variant report

Variant	rs503112
Chromosome Location	chr15:93198513-93198514
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	GABPA	chr15:93198342-93199198	MCF-7	breast:	n/a	chr15:93198921-93198930 chr15:93198473-93198482 chr15:93199099-93199108
2	CTCF	chr15:93198376-93198648	MCF-7	breast:	n/a	chr15:93198483-93198491
3	ZNF143	chr15:93198420-93198571	GM12878	blood:	n/a	chr15:93198511-93198521
4	ELF1	chr15:93198312-93199364	MCF-7	breast:	n/a	chr15:93199043-93199052 chr15:93198982-93198991 chr15:93198983-93198995
5	MAX	chr15:93198249-93199577	H1-hESC	embryonic stem cell:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
6	ELF1	chr15:93198291-93199247	GM12878	blood:	n/a	chr15:93199043-93199052 chr15:93198982-93198991 chr15:93198983-93198995
7	CTCF	chr15:93198460-93198610	HEK293	kidney:	n/a	chr15:93198483-93198491
8	CTCF	chr15:93198440-93198590	GM12870	blood:	n/a	chr15:93198483-93198491
9	POLR2A	chr15:93198376-93199199	GM12878	blood:	n/a	n/a
10	TBP	chr15:93198460-93199006	H1-hESC	embryonic stem cell:	n/a	n/a
11	CTCF	chr15:93198371-93198688	GM12878	blood:	n/a	chr15:93198483-93198491
12	MAX	chr15:93198271-93199489	A549	lung:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
13	PML	chr15:93198351-93199223	MCF-7	breast:	n/a	n/a
14	CTCF	chr15:93198460-93198610	GM12864	blood:	n/a	chr15:93198483-93198491
15	MYC	chr15:93198416-93198674	MCF-7	breast:	n/a	n/a
16	CHD2	chr15:93198481-93198611	H1-hESC	embryonic stem cell:	n/a	n/a
17	CTCF	chr15:93198451-93198580	MCF-7	breast:	n/a	chr15:93198483-93198491
18	RAD21	chr15:93198331-93198563	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr15:93198440-93198590	GM12865	blood:	n/a	chr15:93198483-93198491
20	HDAC2	chr15:93198295-93199446	MCF-7	breast:	n/a	chr15:93198329-93198343
21	RAD21	chr15:93198267-93199198	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr15:93198205-93199327	MCF-7	breast:	n/a	n/a
23	CTCF	chr15:93198405-93198634	MCF-7	breast:	n/a	chr15:93198483-93198491
24	E2F6	chr15:93198346-93199430	A549	lung:	n/a	chr15:93198528-93198540 chr15:93198511-93198520
25	POLR2A	chr15:93198498-93198716	H1-hESC	embryonic stem cell:	n/a	n/a
26	MAX	chr15:93198168-93198778	MCF-7	breast:	n/a	n/a
27	MYC	chr15:93198287-93199268	MCF-7	breast:	n/a	chr15:93199099-93199109 chr15:93199094-93199104 chr15:93199092-93199101 chr15:93199096-93199105 chr15:93199092-93199107
28	CTCF	chr15:93198415-93198607	H1-hESC	embryonic stem cell:	n/a	chr15:93198483-93198491
29	MYC	chr15:93198355-93198702	MCF-7	breast:	n/a	n/a
30	ZNF263	chr15:93198494-93199220	HEK293-T-REx	kidney:	n/a	n/a
31	POLR2A	chr15:93198304-93199182	ECC-1	luminal epithelium:	n/a	n/a
32	YY1	chr15:93198300-93198552	GM12891	blood:	n/a	chr15:93198381-93198392 chr15:93198460-93198474
33	CTCF	chr15:93198401-93198630	MCF-7	breast:	n/a	chr15:93198483-93198491
34	POLR2A	chr15:93198385-93199243	MCF-7	breast:	n/a	n/a
35	CTCF	chr15:93198396-93198600	GM12891	blood:	n/a	chr15:93198483-93198491
36	POLR2A	chr15:93198326-93199219	ECC-1	luminal epithelium:	n/a	n/a
37	CTCF	chr15:93198420-93198570	GM12865	blood:	n/a	chr15:93198483-93198491
38	MXI1	chr15:93198282-93199977	SK-N-SH	brain:	n/a	chr15:93199093-93199102 chr15:93199095-93199104
39	CTCF	chr15:93198485-93198527	Pancreas_OC	pancreas:	n/a	n/a
40	POLR2A	chr15:93198451-93199158	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAZ	chr15:93197964-93198577	GM12878	blood:	n/a	n/a
42	CTCF	chr15:93198440-93198590	GM12871	blood:	n/a	chr15:93198483-93198491
43	ZEB1	chr15:93198313-93198597	GM12878	blood:	n/a	chr15:93198446-93198457 chr15:93198460-93198469
44	EBF1	chr15:93198352-93198618	GM12878	blood:	n/a	n/a
45	CTCF	chr15:93198420-93198570	GM12878	blood:	n/a	chr15:93198483-93198491
46	RAD21	chr15:93198437-93198639	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr15:93198427-93198582	MCF-7	breast:	n/a	chr15:93198483-93198491
48	SIN3AK20	chr15:93198106-93199396	MCF-7	breast:	n/a	n/a
49	ZEB1	chr15:93198241-93198742	GM12878	blood:	n/a	chr15:93198446-93198457 chr15:93198460-93198469
50	POLR2A	chr15:93198373-93199215	GM12878	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:93198495-93198545	AG04450	lung:	fetal
2	chr15:93198495-93198545	HRE	kidney:	n/a
3	chr15:93198495-93198545	RPTEC	kidney:	n/a
4	chr15:93198495-93198545	AG04449	skin:	fetal
5	chr15:93198495-93198545	HCF	heart:	n/a
6	chr15:93198495-93198545	HCM	heart:	n/a
7	chr15:93198495-93198545	U87	brain:	n/a
8	chr15:93198495-93198545	BE2_C	brain:	n/a
9	chr15:93198495-93198545	HL-60	blood:	n/a
10	chr15:93198495-93198545	HEEpiC	esophagus:	n/a
11	chr15:93198495-93198545	HEK293	kidney:	embryo
12	chr15:93198495-93198545	Hela-S3	cervix:	n/a
13	chr15:93198495-93198545	CMK	blood:	n/a
14	chr15:93198495-93198545	GM12892	blood:	n/a
15	chr15:93198495-93198545	K562	blood:	n/a
16	chr15:93198495-93198545	ProgFib	skin:	n/a
17	chr15:93198495-93198545	MCF10A-Er-Src	breast:	n/a
18	chr15:93198495-93198545	GM19239	blood:	n/a
19	chr15:93198495-93198545	SAEC	small airway:	n/a
20	chr15:93198495-93198545	HepG2	liver:	n/a
21	chr15:93198495-93198545	IMR90	lung:	fetal
22	chr15:93198495-93198545	HRCEpiC	kidney:	n/a
23	chr15:93198495-93198545	A549	lung:	n/a
24	chr15:93198495-93198545	PFSK-1	brain:	n/a
25	chr15:93198495-93198545	HIPEpiC	eye:	n/a
26	chr15:93198495-93198545	HCPEpiC	choroid plexus:	n/a
27	chr15:93198495-93198545	HAEpiC	amniotic membrane:	n/a
28	chr15:93198495-93198545	SK-N-SH_RA	brain:	n/a
29	chr15:93198495-93198545	HUVEC	blood vessel:	n/a
30	chr15:93198495-93198545	HCT-116	colon:	n/a
31	chr15:93198495-93198545	PANC-1	pancreas:	n/a
32	chr15:93198495-93198545	AoSMC	blood vessel:	n/a
33	chr15:93198495-93198545	AG10803	skin:	n/a
34	chr15:93198495-93198545	HRPEpiC	eye:	n/a
35	chr15:93198495-93198545	GM12878	blood:	n/a
36	chr15:93198495-93198545	GM06990	blood:	n/a
37	chr15:93198495-93198545	NB4	blood:	n/a
38	chr15:93198495-93198545	Jurkat	blood:	n/a
39	chr15:93198495-93198545	NH-A	brain:	n/a
40	chr15:93198495-93198545	AG09309	skin:	n/a
41	chr15:93198495-93198545	PrEC	prostate:	n/a
42	chr15:93198495-93198545	LNCaP	prostate:	n/a
43	chr15:93198495-93198545	ECC-1	luminal epithelium:	n/a
44	chr15:93198495-93198545	T-47D	breast:	n/a
45	chr15:93198495-93198545	NHDF-neo	bronchial:	n/a
46	chr15:93198495-93198545	AG09319	gingival:	n/a
47	chr15:93198495-93198545	SK-N-MC	brain:	n/a
48	chr15:93198495-93198545	Caco-2	colon:	n/a
49	chr15:93198495-93198545	H1-hESC	embryonic stem cell:	embryo
50	chr15:93198495-93198545	HMEC	breast:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:93145840..93149737-chr15:93196292..93199149,3	MCF-7	breast:
2	chr15:93197537..93199243-chr15:93427702..93429402,2	MCF-7	breast:
3	chr15:93197891..93200562-chr3:14219402..14221003,2	MCF-7	breast:
4	chr15:93187167..93190385-chr15:93197959..93201879,3	K562	blood:

Variant related genes	Relation type
FAM174B	TF binding region
FAM174B	CpG island
ENSG00000272888	Chromatin interaction
ENSG00000271763	Chromatin interaction
ENSG00000185442	Chromatin interaction
ENSG00000154767	Chromatin interaction
ENSG00000170860	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12443091	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908852	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496712	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1496726	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16974307	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2254142	0.89[EUR][1000 genomes]
rs2453901	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs285754	0.87[EUR][1000 genomes]
rs285755	0.88[EUR][1000 genomes]
rs285757	0.88[EUR][1000 genomes]
rs285758	0.88[EUR][1000 genomes]
rs285766	0.80[EUR][1000 genomes]
rs285772	0.90[EUR][1000 genomes]
rs366789	0.82[EUR][1000 genomes]
rs373481	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs406032	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs413450	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs434826	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6496969	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178546	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs893379	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	esv3374130	chr15:93197573-93200121	Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs503112	LOC400451	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93193800-93199000	Enhancers	Fetal Heart	heart
2	chr15:93195200-93199600	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr15:93196600-93199200	Enhancers	Fetal Brain Male	brain
4	chr15:93197000-93199600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr15:93197200-93199000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:93197200-93199400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:93197200-93199400	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr15:93197200-93199600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:93197400-93199400	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr15:93197400-93199600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
11	chr15:93197600-93198600	Flanking Active TSS	Fetal Muscle Trunk	muscle
12	chr15:93197600-93198800	Active TSS	Gastric	stomach
13	chr15:93197600-93199200	Active TSS	HSMM	muscle
14	chr15:93197600-93199400	Active TSS	Pancreas	Pancrea
15	chr15:93197800-93199000	Active TSS	Rectal Mucosa Donor 31	rectum
16	chr15:93197800-93199000	Active TSS	Small Intestine	intestine
17	chr15:93197800-93199200	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr15:93197800-93199200	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr15:93197800-93199200	Active TSS	Brain Cingulate Gyrus	brain
20	chr15:93197800-93199200	Active TSS	Brain Hippocampus Middle	brain
21	chr15:93197800-93199200	Active TSS	Fetal Intestine Small	intestine
22	chr15:93197800-93199200	Active TSS	Stomach Mucosa	stomach
23	chr15:93197800-93199400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
24	chr15:93197800-93199400	Active TSS	Ovary	ovary
25	chr15:93197800-93199600	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr15:93198000-93198600	Enhancers	Primary B cells from peripheral blood	blood
27	chr15:93198000-93199000	Active TSS	ES-I3 Cell Line	embryonic stem cell
28	chr15:93198000-93199000	Active TSS	Brain Angular Gyrus	brain
29	chr15:93198000-93199000	Active TSS	Skeletal Muscle Male	skeletal muscle
30	chr15:93198000-93199000	Bivalent/Poised TSS	Thymus	Thymus
31	chr15:93198000-93199200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:93198000-93199200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:93198000-93199200	Active TSS	Psoas Muscle	Psoas
34	chr15:93198000-93199200	Active TSS	Right Ventricle	heart
35	chr15:93198000-93199400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
36	chr15:93198000-93199400	Active TSS	Colon Smooth Muscle	Colon
37	chr15:93198000-93199600	Active TSS	Rectal Smooth Muscle	rectum
38	chr15:93198200-93198600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr15:93198200-93198600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr15:93198200-93198600	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:93198200-93198600	Flanking Active TSS	Fetal Brain Female	brain
42	chr15:93198200-93198800	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr15:93198200-93199000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr15:93198200-93199000	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr15:93198200-93199000	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr15:93198200-93199000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr15:93198200-93199000	Active TSS	Stomach Smooth Muscle	stomach
48	chr15:93198200-93199200	Active TSS	H9 Cell Line	embryonic stem cell
49	chr15:93198200-93199200	Active TSS	Primary T cells from cord blood	blood
50	chr15:93198200-93199200	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--

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