Variant report

Variant	rs8039105
Chromosome Location	chr15:62359085-62359086
allele	C/T
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	REST	chr15:62358801-62359619	PANC-1	pancreas:	n/a	n/a
2	ATF2	chr15:62358786-62359265	H1-hESC	embryonic stem cell:	n/a	chr15:62359078-62359092
3	REST	chr15:62358890-62359470	PANC-1	pancreas:	n/a	n/a
4	TCF12	chr15:62359059-62359245	H1-hESC	embryonic stem cell:	n/a	n/a
5	CTCF	chr15:62359040-62359190	AG09319	gingival:	n/a	n/a
6	EBF1	chr15:62358898-62359518	GM12878	blood:	n/a	chr15:62359321-62359330 chr15:62359320-62359331 chr15:62359319-62359332
7	MXI1	chr15:62358652-62359556	HepG2	liver:	n/a	chr15:62359052-62359061
8	CTCF	chr15:62359066-62359206	MCF-7	breast:	n/a	n/a
9	CTCF	chr15:62359060-62359210	HRPEpiC	eye:	n/a	n/a
10	REST	chr15:62358985-62359253	Hela-S3	cervix:	n/a	n/a
11	REST	chr15:62359000-62359251	GM12878	blood:	n/a	n/a
12	CTCF	chr15:62359060-62359210	AG04449	skin:	n/a	n/a
13	RUNX3	chr15:62358761-62359108	GM12878	blood:	n/a	n/a
14	MAFK	chr15:62358825-62359261	HepG2	liver:	n/a	chr15:62359035-62359050
15	MYC	chr15:62358914-62359260	MCF-7	breast:	n/a	chr15:62359052-62359062 chr15:62359051-62359064 chr15:62359052-62359063 chr15:62359052-62359063 chr15:62359053-62359062 chr15:62359052-62359062
16	CTCF	chr15:62359020-62359170	AG04449	skin:	n/a	n/a
17	MYC	chr15:62358946-62359242	MCF10A-Er-Src	breast:	n/a	chr15:62359052-62359062 chr15:62359051-62359064 chr15:62359052-62359063 chr15:62359052-62359063 chr15:62359053-62359062 chr15:62359052-62359062
18	MAFK	chr15:62358839-62359261	HepG2	liver:	n/a	chr15:62359035-62359050
19	CTCF	chr15:62359080-62359230	HAc	cerebellar:	n/a	n/a
20	E2F4	chr15:62359041-62359321	GM12878	blood:	n/a	n/a
21	RFX5	chr15:62358950-62359314	HepG2	liver:	n/a	chr15:62359090-62359104 chr15:62359089-62359105
22	CTCF	chr15:62359052-62359229	GM12891	blood:	n/a	n/a
23	RELA	chr15:62358830-62359600	GM19099	blood:	n/a	chr15:62358973-62358982 chr15:62358973-62358982
24	CTCF	chr15:62359026-62359255	MCF-7	breast:	n/a	n/a
25	CTCF	chr15:62359080-62359230	GM12872	blood:	n/a	n/a
26	CTCF	chr15:62359060-62359210	Caco-2	colon:	n/a	n/a
27	ELF1	chr15:62358922-62359231	HepG2	liver:	n/a	n/a
28	REST	chr15:62358955-62359287	PANC-1	pancreas:	n/a	n/a
29	EBF1	chr15:62358856-62359527	GM12878	blood:	n/a	chr15:62359321-62359330 chr15:62359320-62359331 chr15:62359319-62359332
30	CTCF	chr15:62359060-62359210	GM12875	blood:	n/a	n/a
31	CTCF	chr15:62359066-62359219	H1-hESC	embryonic stem cell:	n/a	n/a
32	CTCF	chr15:62359040-62359190	BJ	skin:	n/a	n/a
33	MYC	chr15:62359033-62359173	MCF-7	breast:	n/a	chr15:62359052-62359062 chr15:62359051-62359064 chr15:62359052-62359063 chr15:62359052-62359063 chr15:62359053-62359062 chr15:62359052-62359062
34	CTCF	chr15:62359040-62359190	HPF	lung:	n/a	n/a
35	REST	chr15:62358833-62359803	ECC-1	luminal epithelium:	n/a	n/a
36	REST	chr15:62358894-62359419	MCF-7	breast:	n/a	n/a
37	CTCF	chr15:62359060-62359210	HCPEpiC	choroid plexus:	n/a	n/a
38	SIN3A	chr15:62358791-62359748	H1-hESC	embryonic stem cell:	n/a	chr15:62359052-62359061
39	MAX	chr15:62358871-62359214	GM12878	blood:	n/a	chr15:62359052-62359062 chr15:62359051-62359064 chr15:62359052-62359063 chr15:62359052-62359063 chr15:62359053-62359062 chr15:62359052-62359062
40	CTCF	chr15:62359059-62359178	Fibrobl	skin:	n/a	n/a
41	MAX	chr15:62358772-62359411	HCT-116	colon:	n/a	chr15:62359052-62359062 chr15:62359051-62359064 chr15:62359052-62359063 chr15:62359052-62359063 chr15:62359053-62359062 chr15:62359052-62359062
42	USF1	chr15:62358833-62359325	HCT-116	colon:	n/a	chr15:62359051-62359062
43	MYC	chr15:62358958-62359203	MCF-7	breast:	n/a	chr15:62359052-62359062 chr15:62359051-62359064 chr15:62359052-62359063 chr15:62359052-62359063 chr15:62359053-62359062 chr15:62359052-62359062
44	CTCF	chr15:62359060-62359210	GM12868	blood:	n/a	n/a
45	CTCF	chr15:62359040-62359190	GM12865	blood:	n/a	n/a
46	REST	chr15:62358997-62359279	GM12878	blood:	n/a	n/a
47	MAX	chr15:62358803-62359399	MCF-7	breast:	n/a	chr15:62359052-62359062 chr15:62359051-62359064 chr15:62359052-62359063 chr15:62359052-62359063 chr15:62359053-62359062 chr15:62359052-62359062
48	CTCF	chr15:62359040-62359190	NHDF-neo	bronchial:	n/a	n/a
49	POLR2A	chr15:62359004-62359126	H1-hESC	embryonic stem cell:	n/a	n/a
50	TBP	chr15:62358947-62359456	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
C2CD4A	TF binding region

Extended variants
information (count: 92 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10047986	0.84[EUR][1000 genomes]
rs1030859	0.84[EUR][1000 genomes]
rs10468026	0.85[EUR][1000 genomes]
rs10519157	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11071642	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs11629596	0.86[EUR][1000 genomes]
rs11633500	0.85[EUR][1000 genomes]
rs11634163	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11635977	0.84[EUR][1000 genomes]
rs11635980	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11639482	0.86[CEU][hapmap]
rs12438690	0.82[EUR][1000 genomes]
rs12438803	0.84[EUR][1000 genomes]
rs12439356	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs12440524	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12442212	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs12442675	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs12592402	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs12594658	0.90[CEU][hapmap]
rs12898423	0.81[ASN][1000 genomes]
rs12908081	0.85[CEU][hapmap]
rs12908472	0.81[ASN][1000 genomes]
rs12912348	1.00[YRI][hapmap]
rs12913951	0.84[EUR][1000 genomes]
rs13379492	0.81[ASN][1000 genomes]
rs13379947	0.85[CEU][hapmap]
rs1344601	0.86[CEU][hapmap]
rs1425270	0.86[CEU][hapmap]
rs1436963	0.84[EUR][1000 genomes]
rs1436964	0.84[EUR][1000 genomes]
rs17205365	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs17205407	0.84[EUR][1000 genomes]
rs17205463	0.82[EUR][1000 genomes]
rs17238266	0.81[JPT][hapmap]
rs17271305	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17271340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17271403	0.83[EUR][1000 genomes]
rs17271438	0.82[EUR][1000 genomes]
rs1981916	0.85[CEU][hapmap]
rs2162062	0.86[CEU][hapmap]
rs2414753	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap]
rs2414755	0.85[CEU][hapmap]
rs28411984	0.81[ASN][1000 genomes]
rs28513564	0.83[ASN][1000 genomes]
rs28542204	0.84[EUR][1000 genomes]
rs34096515	0.82[EUR][1000 genomes]
rs35967150	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3784633	0.89[CEU][hapmap]
rs3784634	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4143842	0.83[EUR][1000 genomes]
rs4143843	0.85[EUR][1000 genomes]
rs4564516	0.84[EUR][1000 genomes]
rs4587915	0.89[CEU][hapmap]
rs4774427	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4775453	0.89[CEU][hapmap]
rs4775455	0.90[CEU][hapmap];0.85[EUR][1000 genomes]
rs4775457	0.84[EUR][1000 genomes]
rs4775458	0.84[EUR][1000 genomes]
rs5006593	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs62008532	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162536	0.84[EUR][1000 genomes]
rs7166891	0.82[CEU][hapmap]
rs7170293	0.82[CEU][hapmap]
rs7172967	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7177173	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7177276	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7177711	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs7178424	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7178540	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs7178945	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs731820	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs8025877	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs8026008	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs8027751	0.92[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs8032433	0.81[CEU][hapmap]
rs8034216	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8034335	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs8034914	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs8038932	0.84[EUR][1000 genomes]
rs8039651	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs893156	0.86[CEU][hapmap];0.82[EUR][1000 genomes]
rs893158	0.86[CEU][hapmap];0.83[EUR][1000 genomes]
rs933807	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv457176	chr15:62178695-62519658	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv569643	chr15:62178695-62519658	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv471247	chr15:62202481-62519658	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
4	nsv569646	chr15:62202482-62519658	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv1044748	chr15:62276183-62521856	Active TSS Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	nsv542405	chr15:62276183-62521856	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
7	nsv457178	chr15:62340126-62394324	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv569652	chr15:62340126-62394324	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
9	nsv1560	chr15:62354264-62399304	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:62356600-62360000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
2	chr15:62357200-62360400	Weak transcription	Hela-S3	cervix
3	chr15:62358400-62359600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
4	chr15:62358600-62359200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
5	chr15:62358600-62359200	Bivalent Enhancer	Fetal Heart	heart
6	chr15:62358600-62359400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr15:62358600-62359600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
8	chr15:62358600-62359800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr15:62358600-62360000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr15:62358600-62360000	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
11	chr15:62358600-62360000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:62358600-62360000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
13	chr15:62358600-62360000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
14	chr15:62358600-62360000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:62358600-62360000	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr15:62358600-62360200	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
17	chr15:62358600-62360200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr15:62358600-62360200	Flanking Bivalent TSS/Enh	GM12878-XiMat	blood
19	chr15:62358600-62360200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
20	chr15:62358600-62361000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
21	chr15:62358800-62359200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
22	chr15:62358800-62359200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr15:62358800-62359200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:62358800-62359200	Bivalent/Poised TSS	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:62358800-62359200	Flanking Active TSS	Colonic Mucosa	Colon
26	chr15:62358800-62359200	Bivalent Enhancer	Fetal Stomach	stomach
27	chr15:62358800-62359200	Enhancers	Placenta Amnion	Placenta Amnion
28	chr15:62358800-62359200	Active TSS	Right Atrium	heart
29	chr15:62358800-62359200	Bivalent/Poised TSS	Thymus	Thymus
30	chr15:62358800-62359200	Enhancers	Spleen	Spleen
31	chr15:62358800-62359200	Bivalent Enhancer	A549	lung
32	chr15:62358800-62359400	Active TSS	Breast Myoepithelial Primary Cells	Breast
33	chr15:62358800-62359400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
34	chr15:62358800-62359400	Bivalent Enhancer	Fetal Brain Male	brain
35	chr15:62358800-62359400	Bivalent/Poised TSS	Fetal Brain Female	brain
36	chr15:62358800-62359400	Bivalent Enhancer	Fetal Lung	lung
37	chr15:62358800-62359400	Flanking Active TSS	Psoas Muscle	Psoas
38	chr15:62358800-62359400	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
39	chr15:62358800-62359400	Flanking Active TSS	HUVEC	blood vessel
40	chr15:62358800-62359600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
41	chr15:62358800-62359600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:62358800-62359600	Flanking Bivalent TSS/Enh	Primary T killer naive cells fromperipheralblood	blood
43	chr15:62358800-62359600	Flanking Active TSS	Brain Hippocampus Middle	brain
44	chr15:62358800-62359800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
45	chr15:62358800-62359800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr15:62358800-62359800	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr15:62358800-62359800	Active TSS	Stomach Mucosa	stomach
48	chr15:62358800-62359800	Flanking Bivalent TSS/Enh	Osteobl	bone
49	chr15:62358800-62360000	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
50	chr15:62358800-62360000	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood

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