Variant report

Variant	rs28422875
Chromosome Location	chr15:41136575-41136576
allele	G/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	EGR1	chr15:41135984-41137164	HCT-116	colon:	n/a	chr15:41136535-41136549 chr15:41136188-41136198 chr15:41136183-41136196 chr15:41136186-41136195 chr15:41136183-41136196 chr15:41136183-41136196 chr15:41136184-41136198 chr15:41136537-41136547 chr15:41136184-41136195 chr15:41136183-41136196 chr15:41136185-41136195 chr15:41136536-41136550 chr15:41136602-41136611 chr15:41136184-41136195 chr15:41136535-41136548 chr15:41136183-41136197 chr15:41136185-41136195
2	TCF12	chr15:41136163-41137360	ECC-1	luminal epithelium:	n/a	n/a
3	GTF2F1	chr15:41136335-41136757	H1-hESC	embryonic stem cell:	n/a	n/a
4	SIN3AK20	chr15:41135955-41137422	MCF-7	breast:	n/a	n/a
5	CTBP2	chr15:41135944-41137100	H1-hESC	embryonic stem cell:	n/a	n/a
6	MAX	chr15:41136186-41137423	ECC-1	luminal epithelium:	n/a	chr15:41136188-41136198
7	ZEB1	chr15:41136068-41136859	GM12878	blood:	n/a	chr15:41136372-41136379 chr15:41136370-41136379 chr15:41136646-41136657
8	ELF1	chr15:41136158-41136843	MCF-7	breast:	n/a	chr15:41136197-41136206 chr15:41136192-41136204
9	SPI1	chr15:41136328-41136832	HL-60	blood:	n/a	n/a
10	USF1	chr15:41136220-41136856	ECC-1	luminal epithelium:	n/a	n/a
11	ELF1	chr15:41135827-41137451	GM12878	blood:	n/a	chr15:41136197-41136206 chr15:41136192-41136204 chr15:41135983-41135995
12	RUNX3	chr15:41136400-41137296	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:41136345-41136579	GM12878	blood:	n/a	n/a
14	EBF1	chr15:41136448-41136685	GM12878	blood:	n/a	chr15:41136525-41136536 chr15:41136526-41136535
15	NR2F2	chr15:41136099-41136998	MCF-7	breast:	n/a	n/a
16	POLR2A	chr15:41135912-41137071	MCF-7	breast:	n/a	n/a
17	POLR2A	chr15:41135422-41137445	H1-hESC	embryonic stem cell:	n/a	n/a
18	TAF1	chr15:41135988-41136850	ECC-1	luminal epithelium:	n/a	n/a
19	EP300	chr15:41136081-41137354	ECC-1	luminal epithelium:	n/a	chr15:41136085-41136101 chr15:41136086-41136102 chr15:41136417-41136433 chr15:41136179-41136195
20	POLR2A	chr15:41136145-41136590	K562	blood:	n/a	n/a
21	POLR2A	chr15:41136245-41136797	ProgFib	skin:	n/a	n/a
22	POLR2A	chr15:41135645-41137310	MCF-7	breast:	n/a	n/a
23	YY1	chr15:41136510-41137274	GM12892	blood:	n/a	chr15:41136760-41136780
24	YY1	chr15:41136342-41136600	K562	blood:	n/a	n/a
25	TAF1	chr15:41135862-41137255	ECC-1	luminal epithelium:	n/a	n/a
26	HMGN3	chr15:41135940-41136945	K562	blood:	n/a	chr15:41136237-41136246
27	YY1	chr15:41136207-41137274	ECC-1	luminal epithelium:	n/a	chr15:41136760-41136780
28	GABPA	chr15:41136203-41136740	K562	blood:	n/a	chr15:41136396-41136405
29	POLR2A	chr15:41135866-41136650	K562	blood:	n/a	n/a
30	MAX	chr15:41136234-41136702	K562	blood:	n/a	n/a
31	SPI1	chr15:41136409-41136790	GM12891	blood:	n/a	n/a
32	E2F4	chr15:41136216-41136771	MCF10A-Er-Src	breast:	n/a	chr15:41136420-41136429
33	TAF1	chr15:41135745-41137209	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr15:41135393-41136741	MCF10A-Er-Src	breast:	n/a	n/a
35	ZEB1	chr15:41136190-41136694	HepG2	liver:	n/a	chr15:41136372-41136379 chr15:41136370-41136379 chr15:41136646-41136657
36	HDAC2	chr15:41136211-41136863	MCF-7	breast:	n/a	n/a
37	MAX	chr15:41135442-41137369	HCT-116	colon:	n/a	chr15:41136188-41136198 chr15:41136185-41136194
38	MAZ	chr15:41136013-41136637	K562	blood:	n/a	chr15:41136188-41136198 chr15:41136185-41136194
39	POLR2A	chr15:41135995-41137213	H1-hESC	embryonic stem cell:	n/a	n/a
40	TCF12	chr15:41136011-41137345	ECC-1	luminal epithelium:	n/a	n/a
41	EGR1	chr15:41136058-41136651	K562	blood:	n/a	chr15:41136535-41136549 chr15:41136188-41136198 chr15:41136183-41136196 chr15:41136186-41136195 chr15:41136183-41136196 chr15:41136183-41136196 chr15:41136184-41136198 chr15:41136537-41136547 chr15:41136184-41136195 chr15:41136183-41136196 chr15:41136185-41136195 chr15:41136536-41136550 chr15:41136602-41136611 chr15:41136184-41136195 chr15:41136535-41136548 chr15:41136183-41136197 chr15:41136185-41136195
42	TCF7L2	chr15:41136011-41137058	HCT-116	colon:	n/a	chr15:41136446-41136455
43	ZNF263	chr15:41136269-41137186	K562	blood:	n/a	chr15:41136590-41136611 chr15:41136740-41136749 chr15:41136590-41136599
44	TEAD4	chr15:41136160-41137347	ECC-1	luminal epithelium:	n/a	n/a
45	MYC	chr15:41136374-41136580	K562	blood:	n/a	n/a
46	TAF1	chr15:41136142-41137112	MCF-7	breast:	n/a	n/a
47	ZNF143	chr15:41136455-41136723	GM12878	blood:	n/a	n/a
48	MAZ	chr15:41136353-41136845	GM12878	blood:	n/a	n/a
49	HDAC2	chr15:41136303-41136588	K562	blood:	n/a	n/a
50	ZBTB7A	chr15:41136188-41137205	ECC-1	luminal epithelium:	n/a	chr15:41136391-41136399

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr15:41136556-41136606	GM12891	blood:	n/a
2	chr15:41136556-41136606	MCF10A-Er-Src	breast:	n/a
3	chr15:41136550-41136600	HCF	heart:	n/a
4	chr15:41136550-41136600	ECC-1	luminal epithelium:	n/a
5	chr15:41136550-41136600	NB4	blood:	n/a
6	chr15:41136550-41136600	HL-60	blood:	n/a
7	chr15:41136556-41136606	RPTEC	kidney:	n/a
8	chr15:41136550-41136600	AG09309	skin:	n/a
9	chr15:41136550-41136600	GM12892	blood:	n/a
10	chr15:41136550-41136600	BE2_C	brain:	n/a
11	chr15:41136556-41136606	H1-hESC	embryonic stem cell:	embryo
12	chr15:41136550-41136600	HRPEpiC	eye:	n/a
13	chr15:41136550-41136600	Caco-2	colon:	n/a
14	chr15:41136556-41136606	GM12878	blood:	n/a
15	chr15:41136550-41136600	AG10803	skin:	n/a
16	chr15:41136556-41136606	LNCaP	prostate:	n/a
17	chr15:41136550-41136600	GM19239	blood:	n/a
18	chr15:41136550-41136600	HAEpiC	amniotic membrane:	n/a
19	chr15:41136550-41136600	SK-N-SH_RA	brain:	n/a
20	chr15:41136550-41136600	BJ	skin:	n/a
21	chr15:41136556-41136606	HMEC	breast:	n/a
22	chr15:41136556-41136606	NH-A	brain:	n/a
23	chr15:41136556-41136606	A549	lung:	n/a
24	chr15:41136556-41136606	HCM	heart:	n/a
25	chr15:41136550-41136600	ovcar-3	ovarian:	n/a
26	chr15:41136556-41136606	MCF-7	breast:	n/a
27	chr15:41136550-41136600	MCF-7	breast:	n/a
28	chr15:41136556-41136606	ECC-1	luminal epithelium:	n/a
29	chr15:41136550-41136600	Hepatocyte	liver:	n/a
30	chr15:41136556-41136606	NB4	blood:	n/a
31	chr15:41136556-41136606	HL-60	blood:	n/a
32	chr15:41136556-41136606	AoSMC	blood vessel:	n/a
33	chr15:41136550-41136600	IMR90	lung:	fetal
34	chr15:41136556-41136606	HIPEpiC	eye:	n/a
35	chr15:41136550-41136600	CMK	blood:	n/a
36	chr15:41136550-41136600	HPAEpiC	pulmonary alveolar:	n/a
37	chr15:41136556-41136606	AG04450	lung:	fetal
38	chr15:41136556-41136606	GM12892	blood:	n/a
39	chr15:41136556-41136606	HCPEpiC	choroid plexus:	n/a
40	chr15:41136556-41136606	U87	brain:	n/a
41	chr15:41136550-41136600	AG04449	skin:	fetal
42	chr15:41136556-41136606	SK-N-MC	brain:	n/a
43	chr15:41136550-41136600	AoSMC	blood vessel:	n/a
44	chr15:41136550-41136600	LNCaP	prostate:	n/a
45	chr15:41136550-41136600	AG04450	lung:	fetal
46	chr15:41136550-41136600	Hela-S3	cervix:	n/a
47	chr15:41136550-41136600	T-47D	breast:	n/a
48	chr15:41136550-41136600	GM12878	blood:	n/a
49	chr15:41136550-41136600	HIPEpiC	eye:	n/a
50	chr15:41136550-41136600	A549	lung:	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:41098435..41103357-chr15:41133527..41139132,10	MCF-7	breast:
2	chr15:41134365..41142873-chr15:41160505..41167459,15	MCF-7	breast:
3	chr15:41036541..41039505-chr15:41136514..41138272,3	MCF-7	breast:
4	chr15:41135781..41139367-chr15:41195514..41200270,4	MCF-7	breast:
5	chr15:41135079..41139908-chr15:41161283..41167324,7	MCF-7	breast:
6	chr15:41050847..41052798-chr15:41135268..41136987,2	K562	blood:
7	chr15:41045671..41048162-chr15:41135920..41137784,2	MCF-7	breast:
8	chr15:41120065..41123435-chr15:41135561..41137302,3	MCF-7	breast:
9	chr15:41099271..41102222-chr15:41135281..41137187,2	K562	blood:
10	chr15:41098123..41102222-chr15:41134582..41138137,4	K562	blood:
11	chr15:41135103..41140677-chr15:41182913..41189081,12	MCF-7	breast:
12	chr15:41129275..41132805-chr15:41134409..41137816,5	MCF-7	breast:
13	chr15:40985736..40987452-chr15:41134754..41137017,2	MCF-7	breast:
14	chr15:41095442..41103026-chr15:41134658..41140625,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PPP1R14D-1	chr15:41136377-41136585	ENSG00000261183.1

Variant related genes	Relation type
ENSG00000261183	TF binding region
SPINT1	TF binding region
SPINT1	CpG island
ENSG00000261183	CpG island
ENSG00000166143	Chromatin interaction
ENSG00000251161	Chromatin interaction
ENSG00000104129	Chromatin interaction
ENSG00000261183	Chromatin interaction
ENSG00000137824	Chromatin interaction
ENSG00000166140	Chromatin interaction
ENSG00000104142	Chromatin interaction
ENSG00000051180	Chromatin interaction
ENSG00000245849	Chromatin interaction
ENSG00000104140	Chromatin interaction
ENSG00000271236	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs4924533	1.00[CHB][hapmap]

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	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41135200-41137800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr15:41135200-41138800	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr15:41135200-41139000	Active TSS	Fetal Kidney	kidney
4	chr15:41135400-41137000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
5	chr15:41135400-41137000	Active TSS	Duodenum Mucosa	Duodenum
6	chr15:41135400-41137400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr15:41135400-41137600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr15:41135600-41136800	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:41135600-41136800	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
10	chr15:41135600-41137200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
11	chr15:41135600-41137200	Flanking Active TSS	Colonic Mucosa	Colon
12	chr15:41135600-41137200	Active TSS	Small Intestine	intestine
13	chr15:41135600-41137400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr15:41135600-41137400	Bivalent/Poised TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:41135600-41137400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
16	chr15:41135600-41137600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr15:41135600-41137600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:41135600-41137600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
19	chr15:41135600-41137600	Active TSS	Placenta Amnion	Placenta Amnion
20	chr15:41135600-41138200	Active TSS	Sigmoid Colon	Sigmoid Colon
21	chr15:41135600-41138400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr15:41135600-41138400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:41135600-41138600	Active TSS	Gastric	stomach
24	chr15:41135600-41140200	Active TSS	Rectal Smooth Muscle	rectum
25	chr15:41135600-41140400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:41135800-41136600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr15:41135800-41136800	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:41135800-41136800	Bivalent/Poised TSS	Brain Anterior Caudate	brain
29	chr15:41135800-41136800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
30	chr15:41135800-41136800	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr15:41135800-41137000	Active TSS	Primary T helper naive cells from peripheral blood	blood
32	chr15:41135800-41137200	Active TSS	Ovary	ovary
33	chr15:41135800-41137400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
34	chr15:41135800-41137400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr15:41135800-41137400	Bivalent Enhancer	Fetal Brain Male	brain
36	chr15:41135800-41137400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
37	chr15:41135800-41137400	Flanking Active TSS	Right Ventricle	heart
38	chr15:41135800-41137400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
39	chr15:41135800-41137600	Active TSS	H1 Cell Line	embryonic stem cell
40	chr15:41135800-41137600	Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr15:41135800-41137600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
42	chr15:41135800-41137600	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr15:41135800-41137600	Active TSS	NHEK	skin
44	chr15:41135800-41137800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:41135800-41137800	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr15:41135800-41137800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr15:41135800-41137800	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr15:41135800-41138200	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr15:41135800-41138800	Active TSS	Esophagus	oesophagus
50	chr15:41136000-41136800	Bivalent/Poised TSS	Brain Germinal Matrix	brain

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