Variant report

Variant	rs41435250
Chromosome Location	chr15:74220084-74220085
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	POLR2A	chr15:74219848-74220898	U87	brain:	n/a	n/a
2	TAF1	chr15:74220023-74220274	SK-N-SH	brain:	n/a	n/a
3	EGR1	chr15:74219851-74220385	ECC-1	luminal epithelium:	n/a	chr15:74220351-74220361
4	POLR2A	chr15:74219855-74220928	U87	brain:	n/a	n/a
5	CTCF	chr15:74220060-74220210	GM12866	blood:	n/a	n/a
6	CTCF	chr15:74220080-74220230	AG04449	skin:	n/a	n/a
7	CTCF	chr15:74220019-74220481	MCF-7	breast:	n/a	chr15:74220350-74220366
8	SIN3AK20	chr15:74219548-74221127	MCF-7	breast:	n/a	n/a
9	RAD21	chr15:74220035-74220200	HepG2	liver:	n/a	n/a
10	HA-E2F1	chr15:74219892-74220319	Hela-S3	cervix:	n/a	n/a
11	CTCF	chr15:74220063-74220469	Medullo	brain:	n/a	chr15:74220350-74220366
12	CTCF	chr15:74220037-74220511	A549	lung:	n/a	chr15:74220350-74220366
13	CTCF	chr15:74219992-74220241	Lung_OC	lung:	n/a	n/a
14	RAD21	chr15:74219923-74220613	ECC-1	luminal epithelium:	n/a	chr15:74220387-74220397
15	ZBTB7A	chr15:74219366-74220638	ECC-1	luminal epithelium:	n/a	chr15:74220350-74220359 chr15:74220286-74220294
16	NRF1	chr15:74220053-74220157	GM12878	blood:	n/a	n/a
17	CTCF	chr15:74220061-74220212	GM10266	blood:	n/a	n/a
18	MAX	chr15:74218463-74220913	MCF-7	breast:	n/a	n/a
19	E2F4	chr15:74220075-74220119	MCF10A-Er-Src	breast:	n/a	n/a
20	CTCF	chr15:74219976-74220515	NHEK	skin:	n/a	chr15:74220350-74220366
21	CTCF	chr15:74219918-74220587	MCF-7	breast:	n/a	chr15:74220350-74220366
22	CTCF	chr15:74220023-74220501	K562	blood:	n/a	chr15:74220350-74220366
23	RAD21	chr15:74219946-74220297	HepG2	liver:	n/a	n/a
24	CTCF	chr15:74220028-74220467	GM19238	blood:	n/a	chr15:74220350-74220366
25	CTCF	chr15:74220080-74220230	HEEpiC	esophagus:	n/a	n/a
26	CTCF	chr15:74220032-74220494	GM12892	blood:	n/a	chr15:74220350-74220366
27	EP300	chr15:74219543-74220424	ECC-1	luminal epithelium:	n/a	n/a
28	CTCF	chr15:74219898-74220546	H1-hESC	embryonic stem cell:	n/a	chr15:74220350-74220366
29	CTCF	chr15:74219915-74220535	K562	blood:	n/a	chr15:74220350-74220366
30	CTCF	chr15:74219863-74220764	HCT-116	colon:	n/a	chr15:74220699-74220708 chr15:74220350-74220366
31	PML	chr15:74219866-74220457	MCF-7	breast:	n/a	n/a
32	CTCF	chr15:74220083-74220257	Pancreas_OC	pancreas:	n/a	n/a
33	CTCF	chr15:74219996-74220454	GM12878	blood:	n/a	chr15:74220350-74220366
34	ZBTB7A	chr15:74219034-74220559	ECC-1	luminal epithelium:	n/a	chr15:74220350-74220359 chr15:74220286-74220294
35	CTCF	chr15:74219998-74220502	MCF-7	breast:	n/a	chr15:74220350-74220366
36	CTCF	chr15:74220060-74220210	MCF-7	breast:	n/a	n/a
37	UBTF	chr15:74220011-74220223	K562	blood:	n/a	n/a
38	CTCF	chr15:74220042-74220486	Fibrobl	skin:	n/a	chr15:74220350-74220366
39	MAZ	chr15:74216078-74220816	IMR90	lung:	n/a	n/a
40	NFIC	chr15:74218412-74220406	ECC-1	luminal epithelium:	n/a	n/a
41	POLR2A	chr15:74218425-74220724	ProgFib	skin:	n/a	n/a
42	MXI1	chr15:74217976-74222304	IMR90	lung:	n/a	n/a
43	CTCF	chr15:74220074-74220444	GM12878	blood:	n/a	chr15:74220350-74220366
44	MAX	chr15:74219815-74220377	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr15:74218504-74220498	IMR90	lung:	n/a	n/a
46	EGR1	chr15:74220002-74220303	K562	blood:	n/a	n/a
47	CTCF	chr15:74220053-74220474	MCF-7	breast:	n/a	chr15:74220350-74220366
48	CTCF	chr15:74220014-74220460	LNCaP	prostate:	n/a	chr15:74220350-74220366
49	POLR2A	chr15:74218128-74220905	MCF-7	breast:	n/a	n/a
50	CTCF	chr15:74220062-74220457	K562	blood:	n/a	chr15:74220350-74220366

No.	Distal block	Cell Line	Cell type
1	chr15:74217306..74220336-chr15:74236509..74239961,4	MCF-7	breast:
2	chr15:72523731..72525453-chr15:74219224..74220936,2	MCF-7	breast:
3	chr15:74163735..74170089-chr15:74218002..74222715,6	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STOML1-1	chr15:74219995-74220127	ENSG00000244984
2	lnc-STOML1-1	chr15:74219995-74220127	NONHSAT047178
3	lnc-STOML1-1	chr15:74219995-74220127	NONHSAT047182

Variant related genes	Relation type
LOXL1-AS1	TF binding region
ENSG00000129038	Chromatin interaction
ENSG00000067225	Chromatin interaction
ENSG00000167139	Chromatin interaction
ENSG00000260624	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12594324	0.83[ASN][1000 genomes]
rs12594472	0.85[ASN][1000 genomes]
rs1440101	0.85[ASN][1000 genomes]
rs1550439	0.87[ASN][1000 genomes]
rs16958494	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2304721	0.83[ASN][1000 genomes]
rs28603291	0.85[ASN][1000 genomes]
rs58490364	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73446383	0.80[AMR][1000 genomes];0.86[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	nsv1043335	chr15:74078689-74241186	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv1603	chr15:74191222-74235733	Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	esv2758387	chr15:74215114-74464916	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv2760040	chr15:74215114-74464916	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv428308	chr15:74215114-74464916	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	esv3324978	chr15:74218524-74221272	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74216800-74220800	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr15:74217800-74220400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:74218200-74221200	Active TSS	Aorta	Aorta
4	chr15:74218400-74220400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr15:74218400-74220600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr15:74218400-74220800	Flanking Active TSS	HMEC	breast
7	chr15:74218400-74221000	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr15:74218400-74221200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr15:74218400-74221200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
10	chr15:74218600-74220200	Active TSS	Colon Smooth Muscle	Colon
11	chr15:74218600-74220400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:74218600-74220400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr15:74218600-74220400	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr15:74218600-74220400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
15	chr15:74218600-74220400	Weak transcription	Fetal Heart	heart
16	chr15:74218600-74220600	Active TSS	HUES64 Cell Line	embryonic stem cell
17	chr15:74218600-74220600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr15:74218600-74220600	Active TSS	NHLF	lung
19	chr15:74218600-74220600	Active TSS	Osteobl	bone
20	chr15:74218600-74220800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:74218600-74221000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr15:74218600-74221200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:74218600-74221200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:74218600-74221200	Active TSS	HSMM	muscle
25	chr15:74218600-74221200	Active TSS	NH-A	brain
26	chr15:74218600-74221200	Active TSS	NHDF-Ad	bronchial
27	chr15:74218600-74221400	Active TSS	HSMMtube	muscle
28	chr15:74218800-74220400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr15:74218800-74220400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:74218800-74220400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr15:74218800-74220400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:74218800-74220400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:74218800-74220400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:74218800-74220400	Active TSS	Ovary	ovary
35	chr15:74218800-74220600	Flanking Active TSS	Pancreas	Pancrea
36	chr15:74218800-74220800	Active TSS	Fetal Kidney	kidney
37	chr15:74218800-74221800	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr15:74219000-74220400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr15:74219000-74220400	Bivalent/Poised TSS	Fetal Stomach	stomach
40	chr15:74219000-74220400	Active TSS	Gastric	stomach
41	chr15:74219000-74220400	Active TSS	Left Ventricle	heart
42	chr15:74219000-74220400	Active TSS	Rectal Smooth Muscle	rectum
43	chr15:74219000-74220600	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr15:74219000-74220600	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
45	chr15:74219000-74220600	Active TSS	Fetal Lung	lung
46	chr15:74219000-74220600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
47	chr15:74219200-74220200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
48	chr15:74219200-74220200	Active TSS	Duodenum Smooth Muscle	Duodenum
49	chr15:74219200-74220200	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr15:74219200-74220200	Active TSS	Fetal Intestine Small	intestine

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