Variant report

Variant	rs12899061
Chromosome Location	chr15:78368055-78368056
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	POLR2A	chr15:78368050-78368406	PFSK-1	brain:	n/a	n/a
2	FOXA2	chr15:78367805-78368186	A549	lung:	n/a	n/a
3	CTCF	chr15:78368000-78368150	AG10803	skin:	n/a	n/a
4	CTCF	chr15:78367940-78368090	HCFaa	heart:	n/a	n/a
5	ELF1	chr15:78368024-78368728	MCF-7	breast:	n/a	n/a
6	CTCF	chr15:78367920-78368070	HCPEpiC	choroid plexus:	n/a	n/a
7	MAFK	chr15:78367787-78368847	IMR90	lung:	n/a	chr15:78368155-78368171 chr15:78368160-78368169 chr15:78368153-78368173 chr15:78368156-78368170 chr15:78368158-78368174 chr15:78368158-78368173 chr15:78368157-78368167
8	MAFK	chr15:78367977-78368443	HepG2	liver:	n/a	chr15:78368155-78368171 chr15:78368160-78368169 chr15:78368153-78368173 chr15:78368156-78368170 chr15:78368158-78368174 chr15:78368158-78368173 chr15:78368157-78368167
9	CTCF	chr15:78367980-78368130	HBMEC	blood vessel:	n/a	n/a
10	POLR2A	chr15:78367813-78368181	HUVEC	blood vessel:	n/a	n/a
11	RFX5	chr15:78368033-78368311	Hela-S3	cervix:	n/a	n/a
12	FOS	chr15:78367808-78368295	MCF10A-Er-Src	breast:	n/a	chr15:78368158-78368168
13	GATA3	chr15:78367685-78368615	SK-N-SH	brain:	n/a	n/a
14	CUX1	chr15:78367959-78368133	GM12878	blood:	n/a	n/a
15	CTCF	chr15:78367940-78368090	HVMF	connective:	n/a	n/a
16	FOS	chr15:78367667-78368237	HUVEC	blood vessel:	n/a	chr15:78368158-78368168
17	MAFK	chr15:78367958-78368429	K562	blood:	n/a	chr15:78368155-78368171 chr15:78368160-78368169 chr15:78368153-78368173 chr15:78368156-78368170 chr15:78368158-78368174 chr15:78368158-78368173 chr15:78368157-78368167
18	KAP1	chr15:78367970-78368740	U2OS	brain:	n/a	n/a
19	POLR2A	chr15:78368007-78368489	ProgFib	skin:	n/a	n/a
20	POLR2A	chr15:78367612-78368334	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr15:78367708-78368505	SK-N-SH	brain:	n/a	n/a
22	MAFF	chr15:78367953-78368828	HepG2	liver:	n/a	chr15:78368157-78368175 chr15:78368156-78368170
23	SIN3AK20	chr15:78367801-78368805	MCF-7	breast:	n/a	n/a
24	CREB1	chr15:78368023-78368299	A549	lung:	n/a	n/a
25	MAFK	chr15:78367737-78369024	GM12878	blood:	n/a	chr15:78368155-78368171 chr15:78368160-78368169 chr15:78368153-78368173 chr15:78368156-78368170 chr15:78368158-78368174 chr15:78368158-78368173 chr15:78368157-78368167
26	POLR2A	chr15:78367898-78368425	HUVEC	blood vessel:	n/a	n/a
27	MAFK	chr15:78367876-78368450	HepG2	liver:	n/a	chr15:78368155-78368171 chr15:78368160-78368169 chr15:78368153-78368173 chr15:78368156-78368170 chr15:78368158-78368174 chr15:78368158-78368173 chr15:78368157-78368167
28	GATA2	chr15:78367716-78368058	HUVEC	blood vessel:	n/a	n/a
29	BACH1	chr15:78367961-78368485	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr15:78367712-78370170	IMR90	lung:	n/a	n/a
31	KAP1	chr15:78367875-78368759	HEK293	kidney:	n/a	n/a
32	MAFK	chr15:78367910-78368423	H1-hESC	embryonic stem cell:	n/a	chr15:78368155-78368171 chr15:78368160-78368169 chr15:78368153-78368173 chr15:78368156-78368170 chr15:78368158-78368174 chr15:78368158-78368173 chr15:78368157-78368167
33	RAD21	chr15:78367832-78368794	IMR90	lung:	n/a	n/a
34	CTCF	chr15:78367920-78368070	HMF	breast:	n/a	n/a
35	MAFF	chr15:78367970-78368546	K562	blood:	n/a	chr15:78368157-78368175 chr15:78368156-78368170
36	FOXA1	chr15:78367825-78368168	HepG2	liver:	n/a	n/a
37	MYC	chr15:78367829-78368435	MCF10A-Er-Src	breast:	n/a	n/a
38	CTCF	chr15:78367940-78368090	AG04449	skin:	n/a	n/a
39	REST	chr15:78367839-78368144	SK-N-SH	brain:	n/a	n/a
40	MAFK	chr15:78367940-78368765	Hela-S3	cervix:	n/a	chr15:78368155-78368171 chr15:78368160-78368169 chr15:78368153-78368173 chr15:78368156-78368170 chr15:78368158-78368174 chr15:78368158-78368173 chr15:78368157-78368167
41	ARID3A	chr15:78367952-78368441	HepG2	liver:	n/a	n/a
42	CTCF	chr15:78367980-78368130	HMF	breast:	n/a	n/a
43	ZNF263	chr15:78367875-78369900	HEK293-T-REx	kidney:	n/a	chr15:78369466-78369475 chr15:78368347-78368368 chr15:78369547-78369556
44	JUND	chr15:78367626-78368651	SK-N-SH	brain:	n/a	chr15:78368158-78368168
45	FOXA1	chr15:78367734-78368131	HepG2	liver:	n/a	n/a
46	TCF12	chr15:78367684-78368717	SK-N-SH	brain:	n/a	n/a
47	GATA3	chr15:78367693-78368231	SK-N-SH	brain:	n/a	n/a
48	FOSL2	chr15:78367716-78368408	SK-N-SH	brain:	n/a	chr15:78368158-78368168

No.	Distal block	Cell Line	Cell type
1	chr15:78360126..78361739-chr15:78367541..78369302,2	K562	blood:
2	chr15:78367037..78369598-chr15:78400476..78402359,2	MCF-7	breast:
3	chr15:78357782..78360184-chr15:78367009..78369493,4	MCF-7	breast:
4	chr15:78362119..78363904-chr15:78366538..78368474,2	MCF-7	breast:
5	chr15:78365861..78368679-chr6:26247536..26249940,2	MCF-7	breast:
6	chr15:78303690..78306677-chr15:78365888..78368992,3	MCF-7	breast:
7	chr15:78362996..78365897-chr15:78366671..78369435,4	MCF-7	breast:

Variant related genes	Relation type
SH2D7	TF binding region
ENSG00000167202	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1004855	0.89[AFR][1000 genomes]
rs11631578	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11634607	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11852768	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12148365	0.94[ASN][1000 genomes]
rs12591418	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901812	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12907701	0.93[ASN][1000 genomes]
rs12907814	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12916362	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1348257	0.94[ASN][1000 genomes]
rs1442293	0.93[ASN][1000 genomes]
rs1837913	0.93[ASN][1000 genomes]
rs2044099	0.83[ASN][1000 genomes]
rs2867985	0.95[ASN][1000 genomes]
rs2903702	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3803380	0.97[ASN][1000 genomes]
rs4886553	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886554	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886555	0.95[ASN][1000 genomes]
rs4886994	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4886996	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886999	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4887000	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56317829	0.97[ASN][1000 genomes]
rs57220134	0.93[ASN][1000 genomes]
rs58578288	0.94[ASN][1000 genomes]
rs62011511	0.94[ASN][1000 genomes]
rs7166819	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7170746	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173128	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7181594	0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8029562	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9047	0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 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	chr15:78361400-78368200	Weak transcription	Brain Germinal Matrix	brain
2	chr15:78361600-78369200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:78362800-78369200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:78365000-78368200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr15:78365200-78368200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:78365200-78368200	Weak transcription	Right Ventricle	heart
7	chr15:78365200-78368400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:78365200-78368400	Weak transcription	Fetal Brain Female	brain
9	chr15:78365400-78368400	Weak transcription	Small Intestine	intestine
10	chr15:78366600-78368200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr15:78366800-78369600	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr15:78367000-78368400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr15:78367000-78369000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr15:78367600-78368400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr15:78367600-78368600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
16	chr15:78367600-78369000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:78367600-78369000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr15:78367600-78370400	Active TSS	Ovary	ovary
19	chr15:78367800-78368200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr15:78367800-78368200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:78367800-78368200	Flanking Active TSS	Fetal Kidney	kidney
22	chr15:78367800-78368200	Active TSS	Fetal Muscle Trunk	muscle
23	chr15:78367800-78368200	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
24	chr15:78367800-78368200	Flanking Active TSS	Dnd41	blood
25	chr15:78367800-78368400	Enhancers	Primary hematopoietic stem cells	blood
26	chr15:78367800-78368400	Active TSS	Fetal Intestine Large	intestine
27	chr15:78367800-78368800	Flanking Active TSS	Primary T cells from cord blood	blood
28	chr15:78367800-78368800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr15:78367800-78368800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
30	chr15:78367800-78368800	Flanking Active TSS	HSMM	muscle
31	chr15:78367800-78368800	Flanking Active TSS	NHLF	lung
32	chr15:78367800-78369000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr15:78367800-78369000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:78367800-78369000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr15:78367800-78369000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr15:78367800-78369000	Flanking Active TSS	Liver	Liver
37	chr15:78367800-78369000	Flanking Active TSS	Thymus	Thymus
38	chr15:78367800-78369000	Flanking Active TSS	HepG2	liver
39	chr15:78367800-78369000	Flanking Active TSS	NHEK	skin
40	chr15:78367800-78369200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr15:78367800-78369200	Flanking Active TSS	Placenta	Placenta
42	chr15:78367800-78369200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr15:78367800-78369400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:78367800-78369400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
45	chr15:78367800-78369400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr15:78367800-78369400	Flanking Active TSS	Duodenum Mucosa	Duodenum
47	chr15:78367800-78369400	Flanking Active TSS	Fetal Muscle Leg	muscle
48	chr15:78367800-78369400	Flanking Active TSS	NH-A	brain
49	chr15:78367800-78369400	Flanking Active TSS	Osteobl	bone
50	chr15:78367800-78369600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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