Variant report

Variant	rs41366349
Chromosome Location	chr15:39888889-39888890
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:36)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:36 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:39887671-39889275	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:39887532-39889262	H1-hESC	embryonic stem cell:	n/a	n/a
3	GATA3	chr15:39888485-39888927	MCF-7	breast:	n/a	n/a
4	ESR1	chr15:39888491-39888919	T-47D	breast:	n/a	n/a
5	GATA3	chr15:39888396-39889069	MCF-7	breast:	n/a	n/a
6	POLR2A	chr15:39887572-39888998	HepG2	liver:	n/a	n/a
7	POLR2A	chr15:39870897-39892463	HUVEC	blood vessel:	n/a	n/a
8	CHD1	chr15:39871089-39893027	IMR90	lung:	n/a	chr15:39872910-39872920
9	POLR2A	chr15:39872827-39889306	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr15:39887692-39889213	HepG2	liver:	n/a	n/a
11	GATA2	chr15:39888695-39888926	SH-SY5Y	brain:	n/a	n/a
12	CTCF	chr15:39888740-39888890	AG10803	skin:	n/a	n/a
13	POLR2A	chr15:39888328-39893316	MCF10A-Er-Src	breast:	n/a	n/a
14	GATA3	chr15:39888328-39889101	MCF-7	breast:	n/a	n/a
15	POLR2A	chr15:39888057-39889104	PBDE	blood:	n/a	n/a
16	POLR2A	chr15:39888767-39888933	HepG2	liver:	n/a	n/a
17	E2F4	chr15:39888605-39888965	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr15:39871636-39892218	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr15:39871327-39893495	HUVEC	blood vessel:	n/a	n/a
20	POLR2A	chr15:39887322-39891967	MCF-7	breast:	n/a	n/a
21	GATA3	chr15:39888568-39888901	SH-SY5Y	brain:	n/a	n/a
22	GATA2	chr15:39888196-39888936	HUVEC	blood vessel:	n/a	n/a
23	POLR2A	chr15:39870574-39892778	HUVEC	blood vessel:	n/a	n/a
24	POLR2A	chr15:39871778-39892493	ProgFib	skin:	n/a	n/a
25	ESR1	chr15:39888527-39888906	T-47D	breast:	n/a	n/a
26	POLR2A	chr15:39871484-39892179	HUVEC	blood vessel:	n/a	n/a
27	GATA3	chr15:39888486-39888977	T-47D	breast:	n/a	n/a
28	CTCF	chr15:39888780-39888930	AG10803	skin:	n/a	n/a
29	POLR2A	chr15:39871294-39893132	IMR90	lung:	n/a	n/a
30	POLR2A	chr15:39887700-39889084	A549	lung:	n/a	n/a
31	GATA3	chr15:39888058-39889104	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr15:39888614-39888923	HUVEC	blood vessel:	n/a	n/a
33	POLR2A	chr15:39887685-39889294	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr15:39870624-39892458	HUVEC	blood vessel:	n/a	n/a
35	HDAC2	chr15:39888575-39888922	MCF-7	breast:	n/a	n/a
36	GATA3	chr15:39888564-39888890	T-47D	breast:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:39888267..39889233-chr15:39960437..39961272,3	MCF-7	breast:
2	chr15:39888419..39889256-chr8:90398106..90398973,2	MCF-7	breast:
3	chr15:39888268..39889233-chr15:39960410..39961213,3	MCF-7	breast:
4	chr15:39888505..39890425-chr15:39892076..39894324,2	K562	blood:
5	chr15:39888232..39889117-chr15:39960523..39961284,6	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EIF2AK4-6	chr15:39888536-39890033	ucscGeneNc_uc001zol_2

No data

Variant related genes	Relation type
ENSG00000259279	TF binding region
ENSG00000150667	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16969081	1.00[AMR][1000 genomes]
rs16969293	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]
rs61731228	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:7 , 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
6	nsv1048628	chr15:39877498-39940104	Enhancers Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1502	chr15:39884314-39928968	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:39874800-39889200	Weak transcription	Brain Substantia Nigra	brain
2	chr15:39875000-39889400	Weak transcription	Brain Anterior Caudate	brain
3	chr15:39875200-39889800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:39875600-39889000	Strong transcription	H1 Cell Line	embryonic stem cell
5	chr15:39875600-39890200	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:39875600-39890400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:39875800-39889600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr15:39876200-39890200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr15:39876200-39890400	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:39877200-39890400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:39878000-39890200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:39879800-39889400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:39880200-39889400	ZNF genes & repeats	Fetal Intestine Large	intestine
14	chr15:39880800-39890200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:39881400-39889200	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr15:39882000-39889800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr15:39882200-39889800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr15:39883000-39889000	Strong transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:39884400-39889400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr15:39884800-39890600	Genic enhancers	Rectal Mucosa Donor 31	rectum
21	chr15:39885200-39891000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr15:39886000-39889400	Weak transcription	Stomach Mucosa	stomach
23	chr15:39886000-39889800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr15:39886000-39889800	Weak transcription	Fetal Intestine Small	intestine
25	chr15:39886200-39889600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:39886400-39889000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:39886400-39890800	Weak transcription	Aorta	Aorta
28	chr15:39886600-39889800	Weak transcription	Gastric	stomach
29	chr15:39886600-39890200	Strong transcription	NHLF	lung
30	chr15:39886800-39889200	Strong transcription	NHDF-Ad	bronchial
31	chr15:39886800-39889400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:39886800-39890000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr15:39886800-39890200	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:39887000-39889800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr15:39887000-39891600	Weak transcription	Fetal Brain Male	brain
36	chr15:39887800-39889200	Genic enhancers	Fetal Kidney	kidney
37	chr15:39888000-39889000	Strong transcription	HUVEC	blood vessel
38	chr15:39888000-39889600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr15:39888000-39890000	Weak transcription	Small Intestine	intestine
40	chr15:39888200-39889200	Strong transcription	Osteobl	bone
41	chr15:39888200-39889600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr15:39888200-39890000	Weak transcription	Placenta	Placenta
43	chr15:39888200-39890200	Weak transcription	Colon Smooth Muscle	Colon
44	chr15:39888200-39890200	Strong transcription	NH-A	brain
45	chr15:39888400-39889000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:39888400-39889200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:39888400-39889800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr15:39888400-39889800	Weak transcription	Spleen	Spleen
49	chr15:39888400-39890000	Weak transcription	Colonic Mucosa	Colon
50	chr15:39888400-39890000	Weak transcription	Ovary	ovary

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