Variant report

Variant	rs28368424
Chromosome Location	chr15:52971441-52971442
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	USF1	chr15:52971239-52971905	A549	lung:	n/a	chr15:52971260-52971276 chr15:52971590-52971601 chr15:52971266-52971282 chr15:52971261-52971277
2	POLR2A	chr15:52971343-52971794	SK-N-SH	brain:	n/a	n/a
3	CREB1	chr15:52970220-52971959	HepG2	liver:	n/a	n/a
4	USF1	chr15:52971144-52971784	GM12878	blood:	n/a	chr15:52971177-52971193 chr15:52971260-52971276 chr15:52971590-52971601 chr15:52971266-52971282 chr15:52971261-52971277
5	SPI1	chr15:52971216-52972056	GM12878	blood:	n/a	chr15:52971480-52971493
6	ATF3	chr15:52971385-52971797	H1-hESC	embryonic stem cell:	n/a	chr15:52971712-52971720
7	USF1	chr15:52971338-52971808	A549	lung:	n/a	chr15:52971590-52971601
8	CTCF	chr15:52971420-52971570	BJ	skin:	n/a	n/a
9	POLR2A	chr15:52969910-52971897	MCF10A-Er-Src	breast:	n/a	n/a
10	CREB1	chr15:52971431-52971827	A549	lung:	n/a	n/a
11	MAX	chr15:52971300-52971951	H1-hESC	embryonic stem cell:	n/a	chr15:52971590-52971603 chr15:52971591-52971602 chr15:52971592-52971601 chr15:52971592-52971601 chr15:52971590-52971603 chr15:52971590-52971603
12	CTCF	chr15:52971300-52971450	GM12871	blood:	n/a	n/a
13	EP300	chr15:52971284-52972037	ECC-1	luminal epithelium:	n/a	chr15:52971565-52971575
14	FOSL2	chr15:52970276-52972012	MCF-7	breast:	n/a	chr15:52971115-52971127 chr15:52971116-52971126 chr15:52971708-52971722 chr15:52970749-52970758
15	PAX5	chr15:52971221-52971505	GM12878	blood:	n/a	n/a
16	MAX	chr15:52971049-52972003	ECC-1	luminal epithelium:	n/a	chr15:52971590-52971603 chr15:52971591-52971602 chr15:52971592-52971601 chr15:52971592-52971601 chr15:52971590-52971603 chr15:52971590-52971603
17	EP300	chr15:52971383-52971896	T-47D	breast:	n/a	chr15:52971565-52971575
18	USF1	chr15:52971292-52971914	SK-N-SH	brain:	n/a	chr15:52971590-52971601
19	USF1	chr15:52971134-52971972	HCT-116	colon:	n/a	chr15:52971177-52971193 chr15:52971260-52971276 chr15:52971590-52971601 chr15:52971266-52971282 chr15:52971261-52971277
20	POLR2A	chr15:52971366-52971938	U87	brain:	n/a	n/a
21	MAX	chr15:52970726-52971966	SK-N-SH	brain:	n/a	chr15:52971590-52971603 chr15:52971591-52971602 chr15:52971592-52971601 chr15:52971592-52971601 chr15:52971590-52971603 chr15:52971590-52971603
22	POLR2A	chr15:52970599-52971861	HUVEC	blood vessel:	n/a	n/a
23	GABPA	chr15:52971280-52972007	SK-N-SH	brain:	n/a	n/a
24	MAX	chr15:52971372-52971936	SK-N-SH	brain:	n/a	chr15:52971590-52971603 chr15:52971591-52971602 chr15:52971592-52971601 chr15:52971592-52971601 chr15:52971590-52971603 chr15:52971590-52971603
25	PML	chr15:52970451-52972018	MCF-7	breast:	n/a	n/a
26	TFAP2A	chr15:52970490-52971969	Hela-S3	cervix:	n/a	chr15:52971691-52971702 chr15:52971692-52971700 chr15:52971693-52971701 chr15:52971691-52971702 chr15:52971430-52971438 chr15:52971691-52971702 chr15:52971693-52971701 chr15:52971691-52971702 chr15:52971430-52971438 chr15:52971692-52971700 chr15:52971692-52971700 chr15:52971693-52971701 chr15:52971691-52971702 chr15:52971430-52971438
27	GATA3	chr15:52970179-52972282	MCF-7	breast:	n/a	chr15:52971629-52971639
28	MAX	chr15:52971173-52971905	HepG2	liver:	n/a	chr15:52971590-52971603 chr15:52971591-52971602 chr15:52971592-52971601 chr15:52971592-52971601 chr15:52971590-52971603 chr15:52971590-52971603
29	TCF12	chr15:52970611-52972044	ECC-1	luminal epithelium:	n/a	n/a
30	RUNX3	chr15:52971415-52971811	GM12878	blood:	n/a	n/a
31	POLR2A	chr15:52970216-52971974	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr15:52970513-52971985	H1-hESC	embryonic stem cell:	n/a	n/a
33	SPI1	chr15:52971409-52971797	GM12891	blood:	n/a	chr15:52971480-52971493
34	TBP	chr15:52970445-52971916	H1-hESC	embryonic stem cell:	n/a	n/a
35	USF1	chr15:52971082-52971856	K562	blood:	n/a	chr15:52971177-52971193 chr15:52971260-52971276 chr15:52971590-52971601 chr15:52971266-52971282 chr15:52971261-52971277
36	POLR2A	chr15:52970861-52972001	H1-neurons	neurons:	n/a	n/a
37	MAX	chr15:52970079-52972574	MCF-7	breast:	n/a	chr15:52971590-52971603 chr15:52971591-52971602 chr15:52971592-52971601 chr15:52971592-52971601 chr15:52971590-52971603 chr15:52971590-52971603 chr15:52972284-52972293
38	YY1	chr15:52970918-52971801	K562	blood:	n/a	chr15:52971643-52971657 chr15:52970989-52971000 chr15:52971744-52971766 chr15:52971392-52971401 chr15:52970989-52970998 chr15:52971242-52971253 chr15:52971757-52971765 chr15:52971267-52971281
39	SIN3A	chr15:52970016-52972473	H1-hESC	embryonic stem cell:	n/a	chr15:52970877-52970890 chr15:52970919-52970932 chr15:52970845-52970856 chr15:52971384-52971395 chr15:52971685-52971698
40	CTCF	chr15:52971440-52971590	HCM	heart:	n/a	n/a
41	EP300	chr15:52971385-52971854	T-47D	breast:	n/a	chr15:52971565-52971575
42	MAX	chr15:52971075-52971968	Hela-S3	cervix:	n/a	chr15:52971590-52971603 chr15:52971591-52971602 chr15:52971592-52971601 chr15:52971592-52971601 chr15:52971590-52971603 chr15:52971590-52971603
43	MAX	chr15:52971405-52971881	HUVEC	blood vessel:	n/a	chr15:52971590-52971603 chr15:52971591-52971602 chr15:52971592-52971601 chr15:52971592-52971601 chr15:52971590-52971603 chr15:52971590-52971603
44	POLR2A	chr15:52970611-52972137	MCF-7	breast:	n/a	n/a
45	SIN3AK20	chr15:52971387-52971698	SK-N-SH	brain:	n/a	n/a
46	POLR2A	chr15:52971314-52971899	HCT-116	colon:	n/a	n/a
47	RFX5	chr15:52969780-52972825	SK-N-SH	brain:	n/a	chr15:52971597-52971612 chr15:52971667-52971682 chr15:52971667-52971682 chr15:52969927-52969935 chr15:52971666-52971683 chr15:52971667-52971682
48	FOXA1	chr15:52971425-52971795	T-47D	breast:	n/a	n/a
49	REST	chr15:52970313-52971945	MCF-7	breast:	n/a	chr15:52971230-52971243 chr15:52971486-52971494 chr15:52971688-52971701 chr15:52971479-52971492 chr15:52971365-52971378 chr15:52971178-52971191 chr15:52971472-52971492 chr15:52971368-52971381
50	RFX5	chr15:52970794-52971963	IMR90	lung:	n/a	chr15:52971597-52971612 chr15:52971667-52971682 chr15:52971667-52971682 chr15:52971666-52971683 chr15:52971667-52971682

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:52971398-52971448	AG09309	skin:	n/a
2	chr15:52971398-52971448	RPTEC	kidney:	n/a
3	chr15:52971398-52971448	U87	brain:	n/a
4	chr15:52971398-52971448	AG04450	lung:	fetal
5	chr15:52971398-52971448	CMK	blood:	n/a
6	chr15:52971398-52971448	BJ	skin:	n/a
7	chr15:52971398-52971448	NH-A	brain:	n/a
8	chr15:52971398-52971448	HEEpiC	esophagus:	n/a
9	chr15:52971398-52971448	MCF10A-Er-Src	breast:	n/a
10	chr15:52971398-52971448	MCF-7	breast:	n/a
11	chr15:52971398-52971448	NHBE	bronchial:	n/a
12	chr15:52971398-52971448	HPAEpiC	pulmonary alveolar:	n/a
13	chr15:52971398-52971448	HNPCEpiC	eye:	n/a
14	chr15:52971398-52971448	NB4	blood:	n/a
15	chr15:52971398-52971448	IMR90	lung:	fetal
16	chr15:52971398-52971448	GM19239	blood:	n/a
17	chr15:52971398-52971448	Hepatocyte	liver:	n/a
18	chr15:52971398-52971448	HCPEpiC	choroid plexus:	n/a
19	chr15:52971398-52971448	PFSK-1	brain:	n/a
20	chr15:52971398-52971448	HCF	heart:	n/a
21	chr15:52971398-52971448	PrEC	prostate:	n/a
22	chr15:52971398-52971448	PANC-1	pancreas:	n/a
23	chr15:52971398-52971448	ProgFib	skin:	n/a
24	chr15:52971398-52971448	HMEC	breast:	n/a
25	chr15:52971398-52971448	Caco-2	colon:	n/a
26	chr15:52971398-52971448	HRCEpiC	kidney:	n/a
27	chr15:52971398-52971448	SKMC	muscle:	n/a
28	chr15:52971398-52971448	AG04449	skin:	fetal
29	chr15:52971398-52971448	HRPEpiC	eye:	n/a
30	chr15:52971398-52971448	BE2_C	brain:	n/a
31	chr15:52971398-52971448	AG10803	skin:	n/a
32	chr15:52971398-52971448	SK-N-SH	brain:	n/a
33	chr15:52971398-52971448	A549	lung:	n/a
34	chr15:52971398-52971448	ovcar-3	ovarian:	n/a
35	chr15:52971398-52971448	T-47D	breast:	n/a
36	chr15:52971398-52971448	HCT-116	colon:	n/a
37	chr15:52971398-52971448	HUVEC	blood vessel:	n/a
38	chr15:52971398-52971448	HCM	heart:	n/a
39	chr15:52971398-52971448	Hela-S3	cervix:	n/a
40	chr15:52971398-52971448	NT2-D1	testis:	n/a
41	chr15:52971398-52971448	ECC-1	luminal epithelium:	n/a
42	chr15:52971398-52971448	AoSMC	blood vessel:	n/a
43	chr15:52971398-52971448	LNCaP	prostate:	n/a
44	chr15:52971398-52971448	SK-N-SH_RA	brain:	n/a
45	chr15:52971398-52971448	K562	blood:	n/a
46	chr15:52971398-52971448	AG09319	gingival:	n/a
47	chr15:52971398-52971448	SK-N-MC	brain:	n/a
48	chr15:52971398-52971448	GM12892	blood:	n/a
49	chr15:52971398-52971448	HAEpiC	amniotic membrane:	n/a
50	chr15:52971398-52971448	GM12891	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:52819791..52821534-chr15:52970285..52973265,2	MCF-7	breast:
2	chr15:50645577..50647649-chr15:52968775..52972037,3	MCF-7	breast:
3	chr15:52586831..52588797-chr15:52969729..52971575,2	MCF-7	breast:
4	chr15:52859855..52863944-chr15:52968349..52971887,6	MCF-7	breast:
5	chr15:52967401..52973659-chr15:53000765..53004676,11	MCF-7	breast:
6	chr15:52968259..52973250-chr15:52997483..53005703,18	MCF-7	breast:
7	chr15:52971122..52971700-chr16:68270867..68271650,2	Hela-S3	cervix:
8	chr15:52860660..52861356-chr15:52971076..52971618,2	Hela-S3	cervix:
9	chr15:52855349..52864927-chr15:52966670..52972620,15	MCF-7	breast:
10	chr15:52942408..52952117-chr15:52965431..52973600,32	MCF-7	breast:

Variant related genes	Relation type
FAM214A	TF binding region
FAM214A	CpG island
ENSG00000244879	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000047346	Chromatin interaction
ENSG00000128833	Chromatin interaction
ENSG00000261469	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000197535	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs55703275	0.89[ASN][1000 genomes]
rs7173621	0.89[ASN][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	nsv471245	chr15:52607262-53187165	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv1041421	chr15:52661342-53148286	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv833006	chr15:52825954-53040462	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1049534	chr15:52903314-53022926	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52967400-52972400	Active TSS	Right Atrium	heart
2	chr15:52968400-52972200	Active TSS	Brain Germinal Matrix	brain
3	chr15:52968600-52972200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr15:52968600-52972200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:52969000-52972200	Active TSS	GM12878-XiMat	blood
6	chr15:52969000-52972400	Active TSS	Psoas Muscle	Psoas
7	chr15:52969000-52972400	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr15:52969400-52972200	Active TSS	Aorta	Aorta
9	chr15:52969400-52972200	Active TSS	Fetal Intestine Small	intestine
10	chr15:52969400-52972200	Active TSS	Thymus	Thymus
11	chr15:52969600-52971800	Active TSS	Primary T cells fromperipheralblood	blood
12	chr15:52969600-52972000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:52969600-52972000	Active TSS	Fetal Thymus	thymus
14	chr15:52969600-52972200	Active TSS	Fetal Intestine Large	intestine
15	chr15:52969600-52972200	Active TSS	HMEC	breast
16	chr15:52969600-52972200	Active TSS	NHLF	lung
17	chr15:52969600-52972400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:52969600-52972400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr15:52969800-52972000	Active TSS	Primary T helper cells PMA-I stimulated	--
20	chr15:52969800-52972000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:52969800-52972200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:52969800-52972200	Active TSS	NH-A	brain
23	chr15:52969800-52972200	Active TSS	NHDF-Ad	bronchial
24	chr15:52969800-52972400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:52969800-52972400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:52969800-52972600	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr15:52969800-52972600	Active TSS	HUES6 Cell Line	embryonic stem cell
28	chr15:52969800-52972600	Active TSS	Fetal Kidney	kidney
29	chr15:52969800-52972600	Active TSS	Right Ventricle	heart
30	chr15:52969800-52973000	Active TSS	HSMMtube	muscle
31	chr15:52970000-52972000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:52970000-52972000	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr15:52970000-52972000	Active TSS	Lung	lung
34	chr15:52970000-52972000	Active TSS	Small Intestine	intestine
35	chr15:52970000-52972000	Active TSS	Stomach Mucosa	stomach
36	chr15:52970000-52972000	Active TSS	HSMM	muscle
37	chr15:52970000-52972200	Active TSS	H9 Cell Line	embryonic stem cell
38	chr15:52970000-52972200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:52970000-52972200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr15:52970000-52972200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr15:52970000-52972200	Active TSS	Ovary	ovary
42	chr15:52970000-52972200	Active TSS	Pancreas	Pancrea
43	chr15:52970000-52972200	Active TSS	Sigmoid Colon	Sigmoid Colon
44	chr15:52970000-52972400	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr15:52970000-52972400	Active TSS	Left Ventricle	heart
46	chr15:52970000-52972600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:52970000-52972600	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr15:52970200-52972000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr15:52970200-52972000	Active TSS	Primary T cells from cord blood	blood
50	chr15:52970200-52972000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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