Variant report

Variant	rs61731228
Chromosome Location	chr15:39876313-39876314
allele	A/G
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	CHD2	chr15:39874943-39876670	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:39870897-39892463	HUVEC	blood vessel:	n/a	n/a
3	POLR2A	chr15:39872374-39882964	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr15:39871542-39884619	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr15:39872965-39876755	SK-N-SH	brain:	n/a	n/a
6	POLR2A	chr15:39875836-39876797	HepG2	liver:	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	NRF1	chr15:39876189-39876470	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr15:39875952-39877209	MCF10A-Er-Src	breast:	n/a	n/a
11	ATF2	chr15:39875932-39877265	H1-hESC	embryonic stem cell:	n/a	n/a
12	REST	chr15:39876177-39876385	K562	blood:	n/a	n/a
13	REST	chr15:39876147-39876481	PFSK-1	brain:	n/a	n/a
14	MAZ	chr15:39870877-39886058	IMR90	lung:	n/a	chr15:39874192-39874207 chr15:39872697-39872706 chr15:39873005-39873014
15	POLR2A	chr15:39871578-39884189	H1-hESC	embryonic stem cell:	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	chr15:39872507-39876756	MCF-7	breast:	n/a	n/a
20	REST	chr15:39876250-39876367	K562	blood:	n/a	n/a
21	REST	chr15:39876132-39876472	SK-N-SH	brain:	n/a	n/a
22	POLR2A	chr15:39870574-39892778	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr15:39871778-39892493	ProgFib	skin:	n/a	n/a
24	CTCF	chr15:39876260-39876318	NHEK	skin:	n/a	n/a
25	POLR2A	chr15:39876271-39876443	A549	lung:	n/a	n/a
26	MYC	chr15:39876194-39876442	HUVEC	blood vessel:	n/a	n/a
27	RAD21	chr15:39871133-39876402	IMR90	lung:	n/a	chr15:39872590-39872600 chr15:39872814-39872824 chr15:39872530-39872549 chr15:39873437-39873451
28	POLR2A	chr15:39871484-39892179	HUVEC	blood vessel:	n/a	n/a
29	POLR2A	chr15:39871703-39884436	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr15:39871729-39876746	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr15:39875897-39876948	PBDE	blood:	n/a	n/a
32	POLR2A	chr15:39871294-39893132	IMR90	lung:	n/a	n/a
33	JUND	chr15:39876182-39876455	H1-hESC	embryonic stem cell:	n/a	n/a
34	TAF7	chr15:39871851-39876737	H1-hESC	embryonic stem cell:	n/a	n/a
35	REST	chr15:39876124-39876443	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr15:39876242-39876398	A549	lung:	n/a	n/a
37	POLR2A	chr15:39876271-39876418	A549	lung:	n/a	n/a
38	POLR2A	chr15:39876236-39876477	MCF-7	breast:	n/a	n/a
39	POLR2A	chr15:39871800-39876727	HepG2	liver:	n/a	n/a
40	POLR2A	chr15:39876160-39876420	A549	lung:	n/a	n/a
41	POLR2A	chr15:39871900-39876702	HepG2	liver:	n/a	n/a
42	POLR2A	chr15:39875686-39876696	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr15:39870624-39892458	HUVEC	blood vessel:	n/a	n/a
44	MXI1	chr15:39870632-39876677	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:39462462..39474613-chr15:39871091..39879136,29	MCF-7	breast:
2	chr15:39561763..39569547-chr15:39871861..39876512,9	MCF-7	breast:
3	chr15:39874549..39877059-chr15:39885246..39887766,2	K562	blood:
4	chr15:39875425..39876319-chr15:39923488..39924115,2	MCF-7	breast:
5	chr15:39686331..39688222-chr15:39874533..39876316,2	MCF-7	breast:
6	chr15:39874737..39877413-chr15:39931788..39934836,3	MCF-7	breast:

Variant related genes	Relation type
THBS1	TF binding region
ENSG00000259279	Chromatin interaction
ENSG00000259423	Chromatin interaction
ENSG00000259345	Chromatin interaction
ENSG00000137801	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs16969081	1.00[AMR][1000 genomes]
rs16969293	1.00[AMR][1000 genomes]
rs41366349	1.00[AMR][1000 genomes]
rs4419036	1.00[AMR][1000 genomes]
rs55856565	1.00[AMR][1000 genomes]
rs57158008	1.00[AMR][1000 genomes]
rs57522022	1.00[AMR][1000 genomes]
rs58757397	1.00[AMR][1000 genomes]
rs61694079	1.00[AMR][1000 genomes]
rs7181929	1.00[AMR][1000 genomes]
rs73395254	1.00[AMR][1000 genomes]
rs73395265	1.00[AMR][1000 genomes]
rs74008657	1.00[AMR][1000 genomes]
rs74008679	1.00[AMR][1000 genomes]
rs74008682	1.00[AMR][1000 genomes]
rs74008689	1.00[AMR][1000 genomes]
rs8040050	1.00[AMR][1000 genomes]
rs8041613	1.00[AMR][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:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39872400-39876600	Active TSS	Duodenum Mucosa	Duodenum
2	chr15:39872600-39876800	Active TSS	Small Intestine	intestine
3	chr15:39872600-39882400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:39872800-39877200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr15:39872800-39881600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:39873400-39879200	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr15:39873400-39879400	Weak transcription	Aorta	Aorta
8	chr15:39873400-39879800	Transcr. at gene 5' and 3'	NHDF-Ad	bronchial
9	chr15:39873400-39880800	Transcr. at gene 5' and 3'	NHLF	lung
10	chr15:39873400-39881600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:39873400-39884200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
12	chr15:39873400-39884200	Transcr. at gene 5' and 3'	HUVEC	blood vessel
13	chr15:39873400-39886800	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr15:39873600-39878000	Transcr. at gene 5' and 3'	NHEK	skin
15	chr15:39873600-39882200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
16	chr15:39873600-39882200	Transcr. at gene 5' and 3'	HSMM	muscle
17	chr15:39873600-39884000	Transcr. at gene 5' and 3'	HMEC	breast
18	chr15:39873600-39884000	Transcr. at gene 5' and 3'	Osteobl	bone
19	chr15:39873800-39878400	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
20	chr15:39874000-39876400	Transcr. at gene 5' and 3'	Fetal Lung	lung
21	chr15:39874000-39876800	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
22	chr15:39874000-39877200	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
23	chr15:39874000-39877800	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:39874000-39878000	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
25	chr15:39874000-39879000	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
26	chr15:39874000-39879400	Transcr. at gene 5' and 3'	NH-A	brain
27	chr15:39874000-39879800	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr15:39874200-39876600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:39874200-39876600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
30	chr15:39874200-39876800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr15:39874200-39879200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
32	chr15:39874200-39879400	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:39874400-39876400	Transcr. at gene 5' and 3'	Placenta Amnion	Placenta Amnion
34	chr15:39874600-39876600	Transcr. at gene 5' and 3'	Ovary	ovary
35	chr15:39874600-39880400	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
36	chr15:39874600-39880400	Transcr. at gene 5' and 3'	HSMMtube	muscle
37	chr15:39874800-39876600	Transcr. at gene 5' and 3'	Fetal Kidney	kidney
38	chr15:39874800-39889200	Weak transcription	Brain Substantia Nigra	brain
39	chr15:39875000-39876600	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
40	chr15:39875000-39889400	Weak transcription	Brain Anterior Caudate	brain
41	chr15:39875200-39876800	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr15:39875200-39876800	Weak transcription	Placenta	Placenta
43	chr15:39875200-39877000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:39875200-39880200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr15:39875200-39887800	Strong transcription	H9 Cell Line	embryonic stem cell
46	chr15:39875200-39888400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr15:39875200-39889800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:39875400-39876800	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:39875400-39877600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr15:39875400-39881200	Weak transcription	Skeletal Muscle Male	skeletal muscle

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