Variant report

Variant	rs28372917
Chromosome Location	chr15:75917956-75917957
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	SIN3AK20	chr15:75917544-75918359	H1-hESC	embryonic stem cell:	n/a	n/a
2	HEY1	chr15:75917546-75918956	HepG2	liver:	n/a	chr15:75917721-75917736 chr15:75917732-75917747
3	TEAD4	chr15:75917789-75918487	ECC-1	luminal epithelium:	n/a	n/a
4	ATF3	chr15:75917804-75918167	K562	blood:	n/a	chr15:75918088-75918097
5	POLR2A	chr15:75917379-75918900	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr15:75917402-75918737	GM12878	blood:	n/a	n/a
7	EBF1	chr15:75917616-75918387	GM12878	blood:	n/a	n/a
8	TBL1XR1	chr15:75917826-75918748	K562	blood:	n/a	n/a
9	POLR2A	chr15:75917551-75918773	Hela-S3	cervix:	n/a	n/a
10	CREB1	chr15:75917452-75918322	H1-hESC	embryonic stem cell:	n/a	n/a
11	YY1	chr15:75917555-75918542	HepG2	liver:	n/a	chr15:75918032-75918046 chr15:75918031-75918040 chr15:75917969-75917983 chr15:75918035-75918049 chr15:75918088-75918097 chr15:75917792-75917803 chr15:75918026-75918040 chr15:75917723-75917737
12	POLR2A	chr15:75917398-75918741	PFSK-1	brain:	n/a	n/a
13	MAX	chr15:75917713-75918872	H1-hESC	embryonic stem cell:	n/a	n/a
14	EGR1	chr15:75917840-75918556	H1-hESC	embryonic stem cell:	n/a	chr15:75918078-75918091 chr15:75918086-75918100 chr15:75918087-75918097
15	YY1	chr15:75917576-75918586	GM12878	blood:	n/a	chr15:75918032-75918046 chr15:75918031-75918040 chr15:75917969-75917983 chr15:75918035-75918049 chr15:75918088-75918097 chr15:75917792-75917803 chr15:75918026-75918040 chr15:75917723-75917737
16	TAF1	chr15:75917884-75918709	H1-neurons	neurons:	n/a	n/a
17	NR3C1	chr15:75917424-75918373	A549	lung:	n/a	n/a
18	EP300	chr15:75917667-75918436	HepG2	liver:	n/a	chr15:75918087-75918103 chr15:75918090-75918106 chr15:75917969-75917985
19	USF2	chr15:75917909-75918380	H1-hESC	embryonic stem cell:	n/a	chr15:75918086-75918102 chr15:75918097-75918113 chr15:75917967-75917983 chr15:75918089-75918105 chr15:75918053-75918064
20	SIN3AK20	chr15:75917650-75918044	A549	lung:	n/a	n/a
21	MAX	chr15:75917898-75918284	MCF-7	breast:	n/a	n/a
22	RFX5	chr15:75917843-75918898	Hela-S3	cervix:	n/a	n/a
23	NFIC	chr15:75917640-75918337	HepG2	liver:	n/a	n/a
24	POLR2A	chr15:75917535-75918655	A549	lung:	n/a	n/a
25	TAF1	chr15:75917806-75918452	SK-N-SH	brain:	n/a	n/a
26	TAF1	chr15:75917563-75918181	H1-hESC	embryonic stem cell:	n/a	n/a
27	EGR1	chr15:75917900-75918374	K562	blood:	n/a	chr15:75918078-75918091 chr15:75918086-75918100 chr15:75918087-75918097
28	KAP1	chr15:75917833-75918728	U2OS	brain:	n/a	n/a
29	CREB1	chr15:75917344-75918825	HepG2	liver:	n/a	n/a
30	ATF2	chr15:75917897-75918436	GM12878	blood:	n/a	n/a
31	POLR2A	chr15:75917471-75918803	Raji	blood:	n/a	n/a
32	CEBPB	chr15:75917908-75918413	Hela-S3	cervix:	n/a	n/a
33	POLR2A	chr15:75917373-75918775	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr15:75917421-75918746	K562	blood:	n/a	n/a
35	ELF1	chr15:75917863-75918541	K562	blood:	n/a	chr15:75918033-75918045 chr15:75918195-75918208 chr15:75918031-75918040 chr15:75917976-75917988
36	POLR2A	chr15:75917750-75918662	U87	brain:	n/a	n/a
37	POLR2A	chr15:75917564-75918740	GM12878	blood:	n/a	n/a
38	MAZ	chr15:75917328-75918978	IMR90	lung:	n/a	n/a
39	MAX	chr15:75917746-75918645	Hela-S3	cervix:	n/a	n/a
40	BHLHE40	chr15:75917649-75918586	GM12878	blood:	n/a	chr15:75918086-75918102 chr15:75918097-75918113 chr15:75917967-75917983 chr15:75918089-75918105
41	GTF2F1	chr15:75917899-75918655	K562	blood:	n/a	n/a
42	POLR2A	chr15:75917400-75918825	K562	blood:	n/a	n/a
43	POLR2A	chr15:75917519-75918806	HEK293	kidney:	n/a	n/a
44	GABPA	chr15:75917914-75918410	HepG2	liver:	n/a	chr15:75918088-75918097
45	POLR2A	chr15:75917553-75918762	GM12891	blood:	n/a	n/a
46	TCF12	chr15:75917879-75918208	H1-hESC	embryonic stem cell:	n/a	chr15:75917970-75917977
47	USF1	chr15:75917859-75918335	ECC-1	luminal epithelium:	n/a	chr15:75918086-75918102 chr15:75918097-75918113 chr15:75917967-75917983 chr15:75918089-75918105
48	SP1	chr15:75917580-75918592	K562	blood:	n/a	chr15:75918086-75918098 chr15:75918087-75918101 chr15:75918343-75918364 chr15:75918086-75918098 chr15:75918087-75918097 chr15:75918088-75918097 chr15:75918146-75918157 chr15:75918087-75918096
49	MYC	chr15:75917365-75918426	K562	blood:	n/a	n/a
50	POLR2A	chr15:75917537-75918818	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:75917955-75918005	AG10803	skin:	n/a
2	chr15:75917955-75918005	AG09319	gingival:	n/a
3	chr15:75917955-75918005	PFSK-1	brain:	n/a
4	chr15:75917955-75918005	HPAEpiC	pulmonary alveolar:	n/a
5	chr15:75917955-75918005	HCF	heart:	n/a
6	chr15:75917955-75918005	HCM	heart:	n/a
7	chr15:75917955-75918005	HIPEpiC	eye:	n/a
8	chr15:75917955-75918005	AoSMC	blood vessel:	n/a
9	chr15:75917955-75918005	LNCaP	prostate:	n/a
10	chr15:75917955-75918005	HepG2	liver:	n/a
11	chr15:75917955-75918005	Jurkat	blood:	n/a
12	chr15:75917955-75918005	HRCEpiC	kidney:	n/a
13	chr15:75917955-75918005	RPTEC	kidney:	n/a
14	chr15:75917955-75918005	GM06990	blood:	n/a
15	chr15:75917955-75918005	SK-N-SH	brain:	n/a
16	chr15:75917955-75918005	BJ	skin:	n/a
17	chr15:75917955-75918005	U87	brain:	n/a
18	chr15:75917955-75918005	GM19239	blood:	n/a
19	chr15:75917955-75918005	NHDF-neo	bronchial:	n/a
20	chr15:75917955-75918005	GM12878	blood:	n/a
21	chr15:75917955-75918005	Caco-2	colon:	n/a
22	chr15:75917955-75918005	SK-N-MC	brain:	n/a
23	chr15:75917955-75918005	PANC-1	pancreas:	n/a
24	chr15:75917955-75918005	PrEC	prostate:	n/a
25	chr15:75917955-75918005	GM12892	blood:	n/a
26	chr15:75917955-75918005	HCT-116	colon:	n/a
27	chr15:75917955-75918005	SKMC	muscle:	n/a
28	chr15:75917955-75918005	HRE	kidney:	n/a
29	chr15:75917955-75918005	SAEC	small airway:	n/a
30	chr15:75917955-75918005	MCF10A-Er-Src	breast:	n/a
31	chr15:75917955-75918005	HEK293	kidney:	embryo
32	chr15:75917955-75918005	HEEpiC	esophagus:	n/a
33	chr15:75917955-75918005	GM12891	blood:	n/a
34	chr15:75917955-75918005	AG04449	skin:	fetal
35	chr15:75917955-75918005	ECC-1	luminal epithelium:	n/a
36	chr15:75917955-75918005	AG09309	skin:	n/a
37	chr15:75917955-75918005	SK-N-SH_RA	brain:	n/a
38	chr15:75917955-75918005	HRPEpiC	eye:	n/a
39	chr15:75917955-75918005	NH-A	brain:	n/a
40	chr15:75917955-75918005	CMK	blood:	n/a
41	chr15:75917955-75918005	Hela-S3	cervix:	n/a
42	chr15:75917955-75918005	H1-hESC	embryonic stem cell:	embryo
43	chr15:75917955-75918005	Hepatocyte	liver:	n/a
44	chr15:75917955-75918005	NB4	blood:	n/a
45	chr15:75917955-75918005	T-47D	breast:	n/a
46	chr15:75917955-75918005	HAEpiC	amniotic membrane:	n/a
47	chr15:75917955-75918005	BE2_C	brain:	n/a
48	chr15:75917955-75918005	K562	blood:	n/a
49	chr15:75917955-75918005	HL-60	blood:	n/a
50	chr15:75917955-75918005	ovcar-3	ovarian:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75659095..75662742-chr15:75916445..75919940,7	K562	blood:
2	chr15:75916258..75921824-chr15:75930808..75933710,8	MCF-7	breast:
3	chr15:75743503..75749103-chr15:75916446..75919686,11	K562	blood:
4	chr15:75917263..75918956-chr15:76135075..76137725,2	K562	blood:
5	chr15:75747297..75750090-chr15:75917042..75918594,2	MCF-7	breast:
6	chr15:75916634..75921269-chr15:75928640..75933625,8	MCF-7	breast:
7	chr15:75917668..75918638-chr6:41040003..41040905,2	Hela-S3	cervix:
8	chr15:75660298..75662011-chr15:75917109..75918951,2	MCF-7	breast:
9	chr15:75743363..75745017-chr15:75917841..75919520,2	K562	blood:
10	chr15:75916178..75919035-chr15:75939504..75941880,2	MCF-7	breast:
11	chr15:75745526..75749103-chr15:75915153..75919928,6	K562	blood:
12	chr15:75917766..75918457-chr5:32585566..32586264,2	Hela-S3	cervix:
13	chr15:75652075..75654560-chr15:75917811..75919944,2	K562	blood:
14	chr12:49075625..49076327-chr15:75917685..75918191,2	Hela-S3	cervix:
15	chr12:118454477..118455037-chr15:75917667..75918625,2	Hela-S3	cervix:
16	chr15:75917717..75918662-chr9:125026536..125027365,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SNX33-2	chr15:75917878-75918031	ENSG00000260235.1

Variant related genes	Relation type
SNUPN	TF binding region
SNUPN	CpG island
ENSG00000140367	Chromatin interaction
ENSG00000260274	Chromatin interaction
ENSG00000173548	Chromatin interaction
ENSG00000177971	Chromatin interaction
ENSG00000148187	Chromatin interaction
ENSG00000124596	Chromatin interaction
ENSG00000113387	Chromatin interaction
ENSG00000139620	Chromatin interaction
ENSG00000119446	Chromatin interaction
ENSG00000169375	Chromatin interaction
ENSG00000140400	Chromatin interaction
ENSG00000111445	Chromatin interaction
ENSG00000001167	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1128585	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28372916	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3210683	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886453	0.89[EUR][1000 genomes]
rs4886723	0.94[EUR][1000 genomes]
rs55737327	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56178382	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56267307	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73436854	0.81[EUR][1000 genomes]
rs8025681	0.91[EUR][1000 genomes]
rs8027749	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531901	chr15:75600108-76019966	Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	esv3445070	chr15:75623136-76045948	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	nsv530345	chr15:75628556-75951011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv1048028	chr15:75637515-76019967	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
5	nsv542436	chr15:75637515-76019967	Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	161 gene(s)	inside rSNPs	diseases
6	esv1800424	chr15:75692303-75991451	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
7	nsv531902	chr15:75724505-75919237	Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
8	nsv531903	chr15:75889302-76342128	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
9	esv1813854	chr15:75898640-76002392	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs28372917	CTD-2323K18.1	cis	Thyroid	GTEx
rs28372917	MAN2C1	cis	Whole Blood	GTEx
rs28372917	SNUPN	cis	Thyroid	GTEx
rs28372917	MAN2C1	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75916600-75918400	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr15:75916600-75918400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr15:75916600-75918400	Active TSS	Brain Inferior Temporal Lobe	brain
4	chr15:75916600-75918400	Active TSS	A549	lung
5	chr15:75916800-75918000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:75916800-75918200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:75916800-75918200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:75916800-75918200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:75916800-75918200	Active TSS	NHDF-Ad	bronchial
10	chr15:75916800-75918200	Active TSS	NHLF	lung
11	chr15:75916800-75918400	Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr15:75916800-75918400	Active TSS	Hela-S3	cervix
13	chr15:75916800-75918600	Active TSS	Rectal Mucosa Donor 29	rectum
14	chr15:75916800-75918600	Active TSS	HSMM	muscle
15	chr15:75916800-75918800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:75916800-75919200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr15:75917000-75918000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:75917000-75918200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr15:75917000-75918200	Active TSS	Primary neutrophils fromperipheralblood	blood
20	chr15:75917000-75918200	Active TSS	Primary T cells from cord blood	blood
21	chr15:75917000-75918200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
22	chr15:75917000-75918200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr15:75917000-75918200	Active TSS	Muscle Satellite Cultured Cells	--
24	chr15:75917000-75918200	Active TSS	Adipose Nuclei	Adipose
25	chr15:75917000-75918200	Active TSS	Fetal Muscle Leg	muscle
26	chr15:75917000-75918200	Active TSS	Thymus	Thymus
27	chr15:75917000-75918200	Active TSS	HMEC	breast
28	chr15:75917000-75918200	Active TSS	HSMMtube	muscle
29	chr15:75917000-75918200	Active TSS	HUVEC	blood vessel
30	chr15:75917000-75918200	Active TSS	Osteobl	bone
31	chr15:75917000-75918400	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr15:75917000-75918400	Active TSS	Colonic Mucosa	Colon
33	chr15:75917000-75918400	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr15:75917000-75918400	Active TSS	Fetal Brain Female	brain
35	chr15:75917000-75918400	Active TSS	Fetal Intestine Small	intestine
36	chr15:75917000-75918400	Active TSS	Fetal Stomach	stomach
37	chr15:75917000-75918400	Active TSS	Rectal Mucosa Donor 31	rectum
38	chr15:75917000-75918400	Active TSS	Stomach Smooth Muscle	stomach
39	chr15:75917000-75918400	Active TSS	GM12878-XiMat	blood
40	chr15:75917000-75918600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:75917000-75918600	Active TSS	HUES6 Cell Line	embryonic stem cell
42	chr15:75917000-75918600	Active TSS	HUES64 Cell Line	embryonic stem cell
43	chr15:75917000-75918600	Active TSS	iPS-20b Cell Line	embryonic stem cell
44	chr15:75917000-75918600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr15:75917000-75918600	Active TSS	Brain Angular Gyrus	brain
46	chr15:75917000-75918600	Active TSS	Brain Cingulate Gyrus	brain
47	chr15:75917000-75918600	Active TSS	Brain Hippocampus Middle	brain
48	chr15:75917000-75918600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr15:75917000-75918600	Active TSS	Colon Smooth Muscle	Colon
50	chr15:75917000-75918600	Active TSS	Right Ventricle	heart

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