Variant report

Variant	rs12443060
Chromosome Location	chr15:72491121-72491122
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:107)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:107 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:72489503-72494887	PFSK-1	brain:	n/a	n/a
2	BCL3	chr15:72490013-72491688	A549	lung:	n/a	chr15:72491061-72491070
3	POLR2A	chr15:72490175-72491216	SK-N-MC	brain:	n/a	n/a
4	POLR2A	chr15:72490196-72491882	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:72490200-72491435	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr15:72489689-72496123	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:72489741-72491479	GM18951	blood:	n/a	n/a
8	EP300	chr15:72490426-72491255	A549	lung:	n/a	n/a
9	ATF2	chr15:72490172-72491147	GM12878	blood:	n/a	n/a
10	BCLAF1	chr15:72490198-72491275	GM12878	blood:	n/a	chr15:72491061-72491070
11	POLR2A	chr15:72490679-72491133	A549	lung:	n/a	n/a
12	POLR2A	chr15:72490735-72491159	HepG2	liver:	n/a	n/a
13	JUND	chr15:72490008-72491276	HCT-116	colon:	n/a	n/a
14	POLR2A	chr15:72490228-72501294	GM12878	blood:	n/a	n/a
15	BCL3	chr15:72489954-72491190	GM12878	blood:	n/a	chr15:72491061-72491070
16	POLR2A	chr15:72490186-72491965	GM12892	blood:	n/a	n/a
17	NFATC1	chr15:72490115-72491343	GM12878	blood:	n/a	n/a
18	PML	chr15:72490159-72491750	GM12878	blood:	n/a	n/a
19	POLR2A	chr15:72490100-72491602	GM12892	blood:	n/a	n/a
20	POLR2A	chr15:72490153-72497920	SK-N-SH	brain:	n/a	n/a
21	ELF1	chr15:72490164-72491149	GM12878	blood:	n/a	chr15:72490225-72490237
22	POLR2A	chr15:72489804-72494410	Hela-S3	cervix:	n/a	n/a
23	MTA3	chr15:72490165-72491179	GM12878	blood:	n/a	n/a
24	POLR2A	chr15:72490260-72491615	HepG2	liver:	n/a	n/a
25	POLR2A	chr15:72490151-72491924	GM12891	blood:	n/a	n/a
26	POLR2A	chr15:72490282-72491762	K562	blood:	n/a	n/a
27	POLR2A	chr15:72490685-72491644	K562	blood:	n/a	n/a
28	POLR2A	chr15:72489886-72496219	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr15:72490262-72491342	K562	blood:	n/a	n/a
30	POLR2A	chr15:72490191-72491177	SK-N-SH	brain:	n/a	n/a
31	MYBL2	chr15:72490843-72491361	HepG2	liver:	n/a	n/a
32	SMC3	chr15:72489764-72491276	Hela-S3	cervix:	n/a	chr15:72490300-72490310 chr15:72491235-72491243
33	BCL3	chr15:72490707-72491122	GM12878	blood:	n/a	chr15:72491061-72491070
34	TCF12	chr15:72488885-72491260	A549	lung:	n/a	chr15:72489274-72489282 chr15:72490265-72490275
35	POLR2A	chr15:72488938-72491383	MCF-7	breast:	n/a	n/a
36	POLR2A	chr15:72488935-72491303	ECC-1	luminal epithelium:	n/a	n/a
37	POLR2A	chr15:72488837-72501457	U87	brain:	n/a	n/a
38	POLR2A	chr15:72490172-72491644	GM12878	blood:	n/a	n/a
39	POLR2A	chr15:72488735-72501628	U87	brain:	n/a	n/a
40	POLR2A	chr15:72490001-72501490	GM12891	blood:	n/a	n/a
41	POLR2A	chr15:72489686-72491941	H1-hESC	embryonic stem cell:	n/a	n/a
42	SIN3AK20	chr15:72490201-72491177	A549	lung:	n/a	n/a
43	JUND	chr15:72488981-72491319	A549	lung:	n/a	n/a
44	POLR2A	chr15:72490032-72493676	GM12878	blood:	n/a	n/a
45	POLR2A	chr15:72490460-72491466	HepG2	liver:	n/a	n/a
46	POLR2A	chr15:72489684-72491577	PANC-1	pancreas:	n/a	n/a
47	POLR2A	chr15:72490220-72491799	GM12892	blood:	n/a	n/a
48	MTA3	chr15:72490048-72491602	GM12878	blood:	n/a	n/a
49	POLR2A	chr15:72489652-72494351	K562	blood:	n/a	n/a
50	POLR2A	chr15:72489816-72491742	GM18505	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:72490633..72493001-chr15:72850995..72852624,2	K562	blood:
2	chr15:72484916..72487444-chr15:72490191..72493716,4	MCF-7	breast:
3	chr15:72489508..72492052-chr15:72496693..72498858,2	MCF-7	breast:
4	chr11:8985991..8986779-chr15:72490524..72491472,2	Hela-S3	cervix:
5	chr15:72490651..72493389-chr15:72515368..72517029,2	K562	blood:
6	chr15:72488199..72491266-chr15:72491481..72494588,4	MCF-7	breast:
7	chr15:72487347..72489902-chr15:72491021..72493729,2	K562	blood:
8	chr15:72488604..72491164-chr15:72493836..72495912,3	MCF-7	breast:
9	chr15:72487407..72489902-chr15:72490450..72492521,2	K562	blood:

No data

Variant related genes	Relation type
GRAMD2	TF binding region
ENSG00000067225	Chromatin interaction
ENSG00000175348	Chromatin interaction
ENSG00000254860	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs12441553	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12442820	1.00[ASW][hapmap]
rs8192375	1.00[AFR][1000 genomes];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	nsv431395	chr15:72266174-72701777	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv833051	chr15:72315471-72508429	Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv530817	chr15:72350885-72773374	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
4	esv3430860	chr15:72373723-72849907	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
5	esv3409471	chr15:72488923-72491471	Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:72487600-72493600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:72489200-72491600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr15:72489800-72491600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr15:72489800-72491600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr15:72489800-72491800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr15:72490000-72491200	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:72490000-72491200	Bivalent Enhancer	Fetal Muscle Leg	muscle
8	chr15:72490000-72491400	Weak transcription	Brain Substantia Nigra	brain
9	chr15:72490000-72501800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr15:72490000-72507600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr15:72490200-72491400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr15:72490200-72491400	Genic enhancers	NH-A	brain
13	chr15:72490400-72491200	Genic enhancers	Muscle Satellite Cultured Cells	--
14	chr15:72490400-72491200	Strong transcription	HSMM	muscle
15	chr15:72490400-72491400	Weak transcription	Ovary	ovary
16	chr15:72490400-72491600	Genic enhancers	GM12878-XiMat	blood
17	chr15:72490400-72492800	Weak transcription	Psoas Muscle	Psoas
18	chr15:72490400-72493200	Strong transcription	HSMMtube	muscle
19	chr15:72490400-72495200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr15:72490400-72495400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr15:72490400-72504000	Genic enhancers	A549	lung
22	chr15:72490400-72512000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr15:72490600-72491200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr15:72490600-72491200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:72490600-72491200	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:72490600-72491200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr15:72490600-72491200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
28	chr15:72490600-72491600	Transcr. at gene 5' and 3'	HMEC	breast
29	chr15:72490600-72491600	Transcr. at gene 5' and 3'	NHEK	skin
30	chr15:72490600-72492000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:72490600-72492600	Strong transcription	Right Ventricle	heart
32	chr15:72490600-72493400	Genic enhancers	Fetal Intestine Small	intestine
33	chr15:72490600-72493600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:72490600-72495000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:72490600-72495400	Strong transcription	NHLF	lung
36	chr15:72490600-72495600	Strong transcription	HUVEC	blood vessel
37	chr15:72490600-72497000	Genic enhancers	Stomach Smooth Muscle	stomach
38	chr15:72490600-72498400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr15:72490600-72499400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr15:72490600-72503400	Strong transcription	Primary B cells from cord blood	blood
41	chr15:72490600-72508200	Strong transcription	Primary T helper cells PMA-I stimulated	--
42	chr15:72490600-72512000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:72490600-72513000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr15:72490600-72513200	Strong transcription	Primary B cells from peripheral blood	blood
45	chr15:72490600-72513600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:72490600-72513800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr15:72490600-72515600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:72490600-72518000	Strong transcription	Dnd41	blood
49	chr15:72490800-72491200	Active TSS	Hela-S3	cervix
50	chr15:72490800-72491400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin

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