Variant report

Variant	rs12441319
Chromosome Location	chr15:51200010-51200011
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:224)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:224 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SRF	chr15:51199818-51201357	MCF-7	breast:	n/a	n/a
2	POLR2A	chr15:51199140-51201582	GM18505	blood:	n/a	n/a
3	POLR2A	chr15:51199538-51201132	NB4	blood:	n/a	n/a
4	ELF1	chr15:51199883-51201583	MCF-7	breast:	n/a	chr15:51200871-51200882 chr15:51200607-51200616 chr15:51200872-51200883
5	ZNF143	chr15:51199111-51201036	GM12878	blood:	n/a	n/a
6	SIN3AK20	chr15:51199841-51200184	A549	lung:	n/a	n/a
7	POLR2A	chr15:51199151-51201001	GM12892	blood:	n/a	n/a
8	GATA1	chr15:51199819-51201374	PBDE	blood:	n/a	chr15:51200406-51200415
9	RELA	chr15:51199073-51201031	GM10847	blood:	n/a	n/a
10	FOXA1	chr15:51199915-51200204	T-47D	breast:	n/a	n/a
11	RCOR1	chr15:51199753-51201502	Hela-S3	cervix:	n/a	n/a
12	RUNX3	chr15:51199034-51201100	GM12878	blood:	n/a	n/a
13	JUND	chr15:51199953-51201478	MCF-7	breast:	n/a	n/a
14	RELA	chr15:51199101-51201316	GM15510	blood:	n/a	n/a
15	POLR2A	chr15:51199297-51201667	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr15:51199495-51201269	GM10847	blood:	n/a	n/a
17	ATF2	chr15:51199053-51200228	GM12878	blood:	n/a	n/a
18	RELA	chr15:51199058-51201039	GM19099	blood:	n/a	n/a
19	POLR2A	chr15:51199934-51201372	K562	blood:	n/a	n/a
20	JUN	chr15:51199935-51200108	H1-hESC	embryonic stem cell:	n/a	n/a
21	EP300	chr15:51199740-51200101	K562	blood:	n/a	n/a
22	ZBTB7A	chr15:51199924-51200984	K562	blood:	n/a	n/a
23	MXI1	chr15:51199072-51201696	GM12878	blood:	n/a	n/a
24	EP300	chr15:51199153-51200235	GM12878	blood:	n/a	chr15:51200138-51200152
25	POLR2A	chr15:51200005-51201398	H1-neurons	neurons:	n/a	n/a
26	ATF1	chr15:51199869-51200286	K562	blood:	n/a	n/a
27	SIN3AK20	chr15:51199555-51201560	MCF-7	breast:	n/a	n/a
28	CHD1	chr15:51199896-51200289	H1-hESC	embryonic stem cell:	n/a	n/a
29	TAF1	chr15:51200007-51201095	K562	blood:	n/a	n/a
30	HEY1	chr15:51199871-51201106	HepG2	liver:	n/a	chr15:51200451-51200466 chr15:51200498-51200513
31	RAD21	chr15:51199814-51201738	SK-N-SH	brain:	n/a	chr15:51200797-51200806
32	CTCF	chr15:51199290-51201974	A549	lung:	n/a	chr15:51200799-51200808
33	BCLAF1	chr15:51199038-51201064	GM12878	blood:	n/a	chr15:51200874-51200883 chr15:51200101-51200109 chr15:51200458-51200471
34	MAX	chr15:51199174-51201480	NB4	blood:	n/a	n/a
35	POLR2A	chr15:51199521-51200942	GM12891	blood:	n/a	n/a
36	CHD1	chr15:51199801-51201978	IMR90	lung:	n/a	chr15:51200811-51200820 chr15:51200723-51200732 chr15:51200561-51200568
37	MAX	chr15:51199062-51201501	A549	lung:	n/a	n/a
38	POLR2A	chr15:51199825-51201502	Hela-S3	cervix:	n/a	n/a
39	TAF1	chr15:51200009-51201374	ECC-1	luminal epithelium:	n/a	n/a
40	POLR2A	chr15:51199142-51201485	GM19193	blood:	n/a	n/a
41	IKZF1	chr15:51199275-51200040	GM12878	blood:	n/a	n/a
42	POLR2A	chr15:51199972-51201084	HCT-116	colon:	n/a	n/a
43	MAFK	chr15:51199834-51200103	K562	blood:	n/a	n/a
44	POLR2A	chr15:51199061-51201049	GM12878	blood:	n/a	n/a
45	POLR2A	chr15:51199907-51201124	K562	blood:	n/a	n/a
46	MAX	chr15:51199787-51201883	MCF-7	breast:	n/a	n/a
47	NR2F2	chr15:51199833-51200183	K562	blood:	n/a	n/a
48	MAX	chr15:51199105-51201256	GM12878	blood:	n/a	n/a
49	TBP	chr15:51199123-51200222	GM12878	blood:	n/a	n/a
50	MYC	chr15:51199785-51201069	K562	blood:	n/a	n/a

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:51056442..51059084-chr15:51199726..51202707,2	MCF-7	breast:
2	chr15:50977442..50979922-chr15:51198976..51201748,2	MCF-7	breast:
3	chr15:51183066..51185706-chr15:51196494..51200802,3	K562	blood:
4	chr15:50977828..50980537-chr15:51197788..51202411,5	MCF-7	breast:
5	chr15:51198585..51200191-chr20:47687011..47688512,2	K562	blood:
6	chr15:50645261..50648746-chr15:51197475..51202828,11	MCF-7	breast:
7	chr15:50645568..50648513-chr15:51198882..51201905,4	K562	blood:
8	chr15:50647013..50649194-chr15:51198882..51202798,3	K562	blood:
9	chr15:51199520..51200385-chr17:56756418..56757082,2	Hela-S3	cervix:
10	chr15:51190200..51192622-chr15:51197284..51200160,3	K562	blood:
11	chr15:51054845..51057333-chr15:51198137..51200716,3	K562	blood:
12	chr14:104181567..104182099-chr15:51199828..51200464,2	Hela-S3	cervix:
13	chr15:51199980..51202368-chr15:51206159..51208700,2	MCF-7	breast:
14	chr15:50977199..50981459-chr15:51198510..51202863,6	K562	blood:
15	chr15:50966474..50968190-chr15:51199130..51200749,2	K562	blood:
16	chr15:51191099..51192622-chr15:51197592..51200160,2	K562	blood:
17	chr15:50715057..50718112-chr15:51199966..51202837,4	MCF-7	breast:
18	chr11:62608952..62609548-chr15:51199612..51200235,2	Hela-S3	cervix:
19	chr15:50977199..50979864-chr15:51198670..51201821,3	K562	blood:
20	chr15:50645553..50650972-chr15:51199033..51203961,11	MCF-7	breast:
21	chr15:51055794..51057333-chr15:51198910..51200716,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPPL2A.1-1	chr15:51199113-51200792	NONHSAT042443

No data

Variant related genes	Relation type
AP4E1	TF binding region
ENSG00000081014	Chromatin interaction
ENSG00000200997	Chromatin interaction
ENSG00000126215	Chromatin interaction
ENSG00000138600	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000100711	Chromatin interaction
ENSG00000092439	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000243027	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11070815	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631037	0.92[EUR][1000 genomes]
rs11633226	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635054	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12439323	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619684	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2619685	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28755423	0.92[ASN][1000 genomes]
rs3759808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803369	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3886394	0.83[EUR][1000 genomes]
rs4775912	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4775914	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56289295	0.82[EUR][1000 genomes]
rs7170736	0.81[EUR][1000 genomes]
rs72742336	0.82[EUR][1000 genomes]
rs72742362	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72742383	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72744339	0.92[EUR][1000 genomes]
rs9806270	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043805	chr15:50715572-51208891	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv542384	chr15:50715572-51208891	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
4	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
5	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1042372	chr15:50846461-51208891	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
7	nsv542386	chr15:50846461-51208891	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
8	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
9	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
10	nsv529339	chr15:51048579-51270372	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
11	nsv516168	chr15:51114437-51217361	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
12	nsv428636	chr15:51154834-51298044	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
13	nsv569403	chr15:51191421-51304373	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
14	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51199000-51200200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr15:51199000-51200200	Flanking Active TSS	Liver	Liver
3	chr15:51199000-51201400	Active TSS	Primary T killer memory cells from peripheral blood	blood
4	chr15:51199000-51202000	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr15:51199000-51202400	Active TSS	GM12878-XiMat	blood
6	chr15:51199200-51200200	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr15:51199200-51200400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
8	chr15:51199200-51201400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:51199200-51201400	Active TSS	Stomach Smooth Muscle	stomach
10	chr15:51199200-51201600	Active TSS	Primary T helper cells PMA-I stimulated	--
11	chr15:51199200-51201600	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr15:51199200-51201800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr15:51199200-51201800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr15:51199200-51201800	Active TSS	Colonic Mucosa	Colon
15	chr15:51199200-51202000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:51199200-51202000	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr15:51199200-51202200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:51199200-51202600	Active TSS	Esophagus	oesophagus
19	chr15:51199400-51201200	Active TSS	Primary B cells from peripheral blood	blood
20	chr15:51199400-51201400	Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr15:51199400-51201400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
22	chr15:51199400-51201800	Active TSS	NHDF-Ad	bronchial
23	chr15:51199600-51200200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr15:51199600-51200200	Flanking Active TSS	Adipose Nuclei	Adipose
25	chr15:51199600-51200200	Active TSS	Brain Germinal Matrix	brain
26	chr15:51199600-51200200	Active TSS	Right Atrium	heart
27	chr15:51199600-51200200	Flanking Active TSS	HUVEC	blood vessel
28	chr15:51199600-51200400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr15:51199600-51201400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:51199600-51201600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:51199600-51201600	Active TSS	Lung	lung
32	chr15:51199600-51201800	Active TSS	H1 Cell Line	embryonic stem cell
33	chr15:51199600-51201800	Active TSS	H9 Cell Line	embryonic stem cell
34	chr15:51199600-51201800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr15:51199600-51201800	Active TSS	Fetal Muscle Trunk	muscle
36	chr15:51199600-51201800	Active TSS	Ovary	ovary
37	chr15:51199600-51202000	Active TSS	Psoas Muscle	Psoas
38	chr15:51199600-51202200	Active TSS	Fetal Intestine Small	intestine
39	chr15:51199600-51202600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr15:51199600-51202600	Active TSS	HSMMtube	muscle
41	chr15:51199600-51202800	Active TSS	ES-I3 Cell Line	embryonic stem cell
42	chr15:51199600-51202800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:51199800-51200200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:51199800-51200200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:51199800-51200200	Flanking Active TSS	Primary T cells from cord blood	blood
46	chr15:51199800-51200200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr15:51199800-51200200	Flanking Active TSS	NH-A	brain
48	chr15:51199800-51200400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr15:51199800-51200800	ZNF genes & repeats	Fetal Brain Male	brain
50	chr15:51199800-51201200	Active TSS	Primary T cells fromperipheralblood	blood

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