Variant report

Variant	rs41515347
Chromosome Location	chr15:39874396-39874397
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	chr15:39870897-39892463	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr15:39872374-39882964	HUVEC	blood vessel:	n/a	n/a
3	CTCF	chr15:39874360-39874510	AG09309	skin:	n/a	n/a
4	POLR2A	chr15:39871542-39884619	MCF10A-Er-Src	breast:	n/a	n/a
5	ATF2	chr15:39873011-39874946	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr15:39872965-39876755	SK-N-SH	brain:	n/a	n/a
7	CHD1	chr15:39871089-39893027	IMR90	lung:	n/a	chr15:39872910-39872920
8	POLR2A	chr15:39872827-39889306	SK-N-SH	brain:	n/a	n/a
9	GATA2	chr15:39873871-39874700	HUVEC	blood vessel:	n/a	n/a
10	MAZ	chr15:39870877-39886058	IMR90	lung:	n/a	chr15:39874192-39874207 chr15:39872697-39872706 chr15:39873005-39873014
11	CTCF	chr15:39874280-39874430	NHDF-neo	bronchial:	n/a	chr15:39874333-39874346
12	CHD1	chr15:39871846-39874443	H1-hESC	embryonic stem cell:	n/a	chr15:39872910-39872920
13	TAF7	chr15:39873863-39874490	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr15:39871578-39884189	H1-hESC	embryonic stem cell:	n/a	n/a
15	GATA3	chr15:39872904-39874400	A549	lung:	n/a	n/a
16	POLR2A	chr15:39871636-39892218	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr15:39871327-39893495	HUVEC	blood vessel:	n/a	n/a
18	USF2	chr15:39872488-39877080	H1-hESC	embryonic stem cell:	n/a	chr15:39873437-39873453 chr15:39873434-39873450 chr15:39874194-39874207 chr15:39873397-39873413 chr15:39872593-39872609
19	POLR2A	chr15:39873169-39875621	PBDE	blood:	n/a	n/a
20	POLR2A	chr15:39872507-39876756	MCF-7	breast:	n/a	n/a
21	POLR2A	chr15:39870574-39892778	HUVEC	blood vessel:	n/a	n/a
22	POLR2A	chr15:39871778-39892493	ProgFib	skin:	n/a	n/a
23	RAD21	chr15:39871133-39876402	IMR90	lung:	n/a	chr15:39872590-39872600 chr15:39872814-39872824 chr15:39872530-39872549 chr15:39873437-39873451
24	POLR2A	chr15:39871484-39892179	HUVEC	blood vessel:	n/a	n/a
25	CTCF	chr15:39874280-39874430	HAc	cerebellar:	n/a	chr15:39874333-39874346
26	POLR2A	chr15:39871703-39884436	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr15:39871729-39876746	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr15:39871294-39893132	IMR90	lung:	n/a	n/a
29	TAF7	chr15:39871851-39876737	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr15:39874364-39874955	A549	lung:	n/a	n/a
31	POLR2A	chr15:39872367-39875111	MCF-7	breast:	n/a	n/a
32	MAX	chr15:39873760-39874407	MCF-7	breast:	n/a	chr15:39874192-39874207
33	SIN3AK20	chr15:39871527-39875469	MCF-7	breast:	n/a	n/a
34	SMC3	chr15:39870801-39874615	SK-N-SH	brain:	n/a	chr15:39873146-39873160 chr15:39872057-39872071
35	POLR2A	chr15:39871903-39874598	MCF10A-Er-Src	breast:	n/a	n/a
36	CTCF	chr15:39872019-39874442	SK-N-SH	brain:	n/a	chr15:39872533-39872549 chr15:39873503-39873512 chr15:39872532-39872550 chr15:39874333-39874346 chr15:39873147-39873160
37	POLR2A	chr15:39872479-39875248	H1-hESC	embryonic stem cell:	n/a	n/a
38	POLR2A	chr15:39871800-39876727	HepG2	liver:	n/a	n/a
39	POLR2A	chr15:39871900-39876702	HepG2	liver:	n/a	n/a
40	CTCF	chr15:39874260-39874410	GM12864	blood:	n/a	chr15:39874333-39874346
41	POLR2A	chr15:39870624-39892458	HUVEC	blood vessel:	n/a	n/a
42	MXI1	chr15:39870632-39876677	IMR90	lung:	n/a	n/a
43	CTCF	chr15:39874380-39874530	BJ	skin:	n/a	n/a
44	CTCF	chr15:39873865-39874451	IMR90	lung:	n/a	chr15:39874333-39874346

No.	Distal block	Cell Line	Cell type
1	chr15:39462462..39474613-chr15:39871091..39879136,29	MCF-7	breast:
2	chr15:39705799..39707909-chr15:39873297..39874835,2	MCF-7	breast:
3	chr15:39694348..39696610-chr15:39874084..39875864,2	MCF-7	breast:
4	chr15:39561763..39569547-chr15:39871861..39876512,9	MCF-7	breast:
5	chr15:39457550..39462148-chr15:39871822..39875383,4	MCF-7	breast:
6	chr15:39562139..39567868-chr15:39871478..39875404,11	MCF-7	breast:
7	chr15:38997651..39000510-chr15:39873300..39874931,2	MCF-7	breast:
8	chr15:39869407..39871427-chr15:39874178..39876262,2	K562	blood:
9	chr15:39872681..39874712-chr15:39877108..39879648,2	K562	blood:
10	chr15:39873532..39876107-chr15:39899045..39902121,3	MCF-7	breast:
11	chr15:39873342..39875967-chr15:39918932..39920569,2	MCF-7	breast:
12	chr15:39873411..39875536-chr15:39928177..39929699,2	MCF-7	breast:
13	chr15:39873405..39876255-chr15:39978051..39980636,2	MCF-7	breast:

Variant related genes	Relation type
THBS1	TF binding region
ENSG00000259345	Chromatin interaction
ENSG00000137801	Chromatin interaction
ENSG00000259423	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10083552	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10520136	0.83[ASN][1000 genomes]
rs12324682	0.83[ASN][1000 genomes]
rs16969307	1.00[EUR][1000 genomes]
rs16969335	0.83[ASN][1000 genomes]
rs16969338	0.83[ASN][1000 genomes]
rs16969352	0.83[ASN][1000 genomes]
rs16969364	1.00[EUR][1000 genomes]
rs16969365	1.00[EUR][1000 genomes]
rs16969384	1.00[EUR][1000 genomes]
rs16969484	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16969573	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16969678	0.83[ASN][1000 genomes]
rs41376748	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41406047	1.00[EUR][1000 genomes]
rs4291886	1.00[ASN][1000 genomes]
rs4322636	0.83[ASN][1000 genomes]
rs58677957	1.00[EUR][1000 genomes]
rs58716252	1.00[EUR][1000 genomes]
rs59146042	1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61040173	0.80[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163020	1.00[EUR][1000 genomes]
rs7172057	1.00[EUR][1000 genomes]
rs74008705	1.00[EUR][1000 genomes]
rs8023525	1.00[EUR][1000 genomes]
rs8029417	1.00[EUR][1000 genomes]
rs8030643	1.00[EUR][1000 genomes]
rs8031289	1.00[EUR][1000 genomes]
rs8033803	1.00[EUR][1000 genomes]
rs8035627	1.00[EUR][1000 genomes]
rs8036035	0.83[ASN][1000 genomes]
rs8043342	1.00[EUR][1000 genomes]
rs878941	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1049682	chr15:39657279-40027403	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv542361	chr15:39657279-40027403	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv3373125	chr15:39691567-40061262	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904094	chr15:39738006-39976057	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv832977	chr15:39817512-39981520	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39871600-39875400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:39871600-39875400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:39871800-39874400	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr15:39871800-39874400	Active TSS	Left Ventricle	heart
5	chr15:39871800-39874400	Active TSS	Placenta Amnion	Placenta Amnion
6	chr15:39871800-39874800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:39871800-39874800	Active TSS	Fetal Kidney	kidney
8	chr15:39871800-39875200	Active TSS	Gastric	stomach
9	chr15:39872200-39875200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
10	chr15:39872400-39874600	Active TSS	HUES64 Cell Line	embryonic stem cell
11	chr15:39872400-39874600	Active TSS	HSMMtube	muscle
12	chr15:39872400-39874800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr15:39872400-39875000	Active TSS	Brain Anterior Caudate	brain
14	chr15:39872400-39876600	Active TSS	Duodenum Mucosa	Duodenum
15	chr15:39872600-39874400	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr15:39872600-39874600	Flanking Active TSS	Liver	Liver
17	chr15:39872600-39876800	Active TSS	Small Intestine	intestine
18	chr15:39872600-39882400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:39872800-39874400	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
20	chr15:39872800-39874600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
21	chr15:39872800-39875400	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr15:39872800-39875400	Active TSS	Psoas Muscle	Psoas
23	chr15:39872800-39875600	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
24	chr15:39872800-39877200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:39872800-39881600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:39873000-39874400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
27	chr15:39873200-39874800	Bivalent/Poised TSS	Thymus	Thymus
28	chr15:39873400-39874400	Flanking Bivalent TSS/Enh	Fetal Brain Male	brain
29	chr15:39873400-39875000	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr15:39873400-39875000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
31	chr15:39873400-39879200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:39873400-39879400	Weak transcription	Aorta	Aorta
33	chr15:39873400-39879800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
34	chr15:39873400-39880800	Transcr. at gene 5' and 3'	NHLF	lung
35	chr15:39873400-39881600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:39873400-39884200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
37	chr15:39873400-39884200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
38	chr15:39873400-39886800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr15:39873600-39874400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:39873600-39874600	Active TSS	Right Atrium	heart
41	chr15:39873600-39876000	Active TSS	Fetal Brain Female	brain
42	chr15:39873600-39878000	Transcr. at gene 5' and 3'	NHEK	skin
43	chr15:39873600-39882200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
44	chr15:39873600-39882200	Transcr. at gene 5' and 3'	HSMM	muscle
45	chr15:39873600-39884000	Transcr. at gene 5' and 3'	HMEC	breast
46	chr15:39873600-39884000	Transcr. at gene 5' and 3'	Osteobl	bone
47	chr15:39873800-39874400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
48	chr15:39873800-39874400	Bivalent/Poised TSS	Primary B cells from cord blood	blood
49	chr15:39873800-39874600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
50	chr15:39873800-39875200	Transcr. at gene 5' and 3'	H1 Derived Mesenchymal Stem Cells	ES cell derived

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