Variant report

Variant	rs2278519
Chromosome Location	chr15:93258310-93258311
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	CTCF	chr15:93258160-93258310	HMEC	breast:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
2	CTCF	chr15:93258098-93258353	LNCaP	prostate:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
3	YY1	chr15:93257717-93258324	SK-N-SH	brain:	n/a	chr15:93258147-93258161 chr15:93258222-93258230 chr15:93257946-93257955 chr15:93257906-93257920 chr15:93258219-93258241 chr15:93258108-93258119
4	CTCF	chr15:93258083-93258312	MCF-7	breast:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
5	RAD21	chr15:93257813-93258529	MCF-7	breast:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996 chr15:93257849-93257863
6	RCOR1	chr15:93258074-93258406	K562	blood:	n/a	n/a
7	CTCF	chr15:93257824-93258516	IMR90	lung:	n/a	chr15:93257849-93257862 chr15:93258213-93258234 chr15:93257847-93257865 chr15:93257853-93257862 chr15:93258219-93258235 chr15:93258218-93258236
8	BHLHE40	chr15:93258053-93258381	GM12878	blood:	n/a	n/a
9	CTCF	chr15:93258077-93258388	GM12878	blood:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
10	CTCF	chr15:93258096-93258319	A549	lung:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
11	RAD21	chr15:93258088-93258416	K562	blood:	n/a	chr15:93258216-93258235 chr15:93258222-93258231
12	HA-E2F1	chr15:93257484-93258443	MCF-7	breast:	n/a	chr15:93257842-93257854 chr15:93258165-93258172 chr15:93258160-93258175 chr15:93258112-93258122 chr15:93258211-93258226
13	EBF1	chr15:93258070-93258397	GM12878	blood:	n/a	n/a
14	CTCF	chr15:93258067-93258348	Gliobla	brain:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
15	CTCF	chr15:93257937-93258355	K562	blood:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
16	NRF1	chr15:93258088-93258406	GM12878	blood:	n/a	n/a
17	MAX	chr15:93257743-93258435	H1-hESC	embryonic stem cell:	n/a	n/a
18	CTCF	chr15:93258160-93258310	GM12870	blood:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
19	ZNF143	chr15:93257817-93258406	GM12878	blood:	n/a	chr15:93258144-93258162
20	CTCF	chr15:93258240-93258390	GM12868	blood:	n/a	n/a
21	BACH1	chr15:93257518-93258323	H1-hESC	embryonic stem cell:	n/a	n/a
22	REST	chr15:93257686-93258352	A549	lung:	n/a	n/a
23	MAX	chr15:93257978-93258381	GM12878	blood:	n/a	n/a
24	RAD21	chr15:93257267-93258622	MCF-7	breast:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996 chr15:93257849-93257863
25	CTCF	chr15:93258200-93258350	HEK293	kidney:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
26	SMC3	chr15:93258016-93258423	Hela-S3	cervix:	n/a	chr15:93258220-93258234
27	CTCF	chr15:93258160-93258310	GM12878	blood:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
28	CTCF	chr15:93258160-93258310	NHDF-neo	bronchial:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
29	BRCA1	chr15:93258133-93258510	H1-hESC	embryonic stem cell:	n/a	n/a
30	CTCF	chr15:93258010-93258416	A549	lung:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
31	POLR2A	chr15:93257684-93258339	HUVEC	blood vessel:	n/a	n/a
32	CTCF	chr15:93258180-93258330	WERI-Rb-1	eye:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
33	MAZ	chr15:93258060-93258373	K562	blood:	n/a	n/a
34	RAD21	chr15:93257926-93258452	A549	lung:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996
35	ZBTB7A	chr15:93257662-93258499	ECC-1	luminal epithelium:	n/a	chr15:93258159-93258166
36	CTCF	chr15:93258160-93258310	HMF	breast:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
37	E2F4	chr15:93258110-93258430	GM12878	blood:	n/a	chr15:93258165-93258172 chr15:93258160-93258175 chr15:93258112-93258122 chr15:93258211-93258226
38	CTCF	chr15:93258180-93258330	HepG2	liver:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
39	CTCF	chr15:93258180-93258330	HBMEC	blood vessel:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
40	RAD21	chr15:93258006-93258434	A549	lung:	n/a	chr15:93258216-93258235 chr15:93258222-93258231
41	MAX	chr15:93257523-93258503	A549	lung:	n/a	n/a
42	CTCF	chr15:93258036-93258331	SK-N-SH_RA	brain:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
43	SP4	chr15:93257916-93258350	H1-hESC	embryonic stem cell:	n/a	n/a
44	TCF12	chr15:93257192-93258497	A549	lung:	n/a	chr15:93257767-93257774 chr15:93258112-93258122
45	CTCF	chr15:93258180-93258330	HCFaa	heart:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
46	CTCF	chr15:93258180-93258330	GM12801	blood:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
47	RAD21	chr15:93257781-93258419	SK-N-SH_RA	brain:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996 chr15:93257849-93257863
48	TBP	chr15:93257427-93258338	H1-hESC	embryonic stem cell:	n/a	n/a
49	MAX	chr15:93257989-93258380	H1-hESC	embryonic stem cell:	n/a	n/a
50	MAX	chr15:93257167-93258509	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:93155302..93156114-chr15:93257721..93258317,3	MCF-7	breast:
2	chr15:93237040..93237940-chr15:93257791..93258641,4	MCF-7	breast:
3	chr15:93258240..93259897-chr15:93272535..93274240,2	MCF-7	breast:
4	chr15:93237881..93239746-chr15:93257502..93259973,2	MCF-7	breast:
5	chr15:93191617..93195403-chr15:93257490..93261490,4	MCF-7	breast:
6	chr15:92640503..92641006-chr15:93257734..93258635,2	K562	blood:
7	chr15:93195935..93200377-chr15:93256556..93260471,5	MCF-7	breast:
8	chr15:93226419..93227336-chr15:93257734..93258779,3	MCF-7	breast:
9	chr15:93252649..93254753-chr15:93257319..93260184,2	MCF-7	breast:
10	chr15:93064480..93065790-chr15:93258050..93258792,4	MCF-7	breast:
11	chr15:93064431..93065465-chr15:93257828..93258686,4	MCF-7	breast:
12	chr15:93187273..93189424-chr15:93256884..93259260,2	MCF-7	breast:
13	chr15:93236752..93237933-chr15:93257714..93258936,17	MCF-7	breast:

Variant related genes	Relation type
ENSG00000240484	TF binding region
ENSG00000185442	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1004309	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11854403	0.90[EUR][1000 genomes]
rs11854426	0.90[EUR][1000 genomes]
rs12439654	0.82[ASN][1000 genomes]
rs12440201	0.82[ASN][1000 genomes]
rs12440617	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12441089	0.81[EUR][1000 genomes]
rs12442362	0.82[ASN][1000 genomes]
rs12442555	0.82[ASN][1000 genomes]
rs12899027	0.89[EUR][1000 genomes]
rs12906973	0.88[ASN][1000 genomes]
rs1545143	0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs1561304	0.93[ASN][1000 genomes]
rs17648050	0.84[CHD][hapmap];0.92[ASN][1000 genomes]
rs1808818	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1971808	0.86[EUR][1000 genomes]
rs2018744	0.86[EUR][1000 genomes]
rs2278520	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2278521	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2387911	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2387913	0.85[EUR][1000 genomes]
rs2387914	0.84[EUR][1000 genomes]
rs2387915	0.91[EUR][1000 genomes]
rs34888918	0.88[EUR][1000 genomes]
rs34981968	0.89[EUR][1000 genomes]
rs35095971	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35244027	0.89[EUR][1000 genomes]
rs35257450	0.81[EUR][1000 genomes]
rs35663415	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35770033	0.89[EUR][1000 genomes]
rs35982819	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4777731	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4777734	0.91[EUR][1000 genomes]
rs4778033	0.89[ASN][1000 genomes]
rs4778034	0.89[EUR][1000 genomes]
rs57030748	0.87[EUR][1000 genomes]
rs58407306	0.88[EUR][1000 genomes]
rs58894958	0.87[ASN][1000 genomes]
rs60471977	0.91[EUR][1000 genomes]
rs6496972	0.85[EUR][1000 genomes]
rs6496973	0.91[EUR][1000 genomes]
rs6496974	0.91[EUR][1000 genomes]
rs6496975	0.91[EUR][1000 genomes]
rs6496976	0.91[EUR][1000 genomes]
rs6496977	0.89[EUR][1000 genomes]
rs6496978	0.90[EUR][1000 genomes]
rs6496979	0.90[EUR][1000 genomes]
rs6496982	0.89[EUR][1000 genomes]
rs6496985	0.87[EUR][1000 genomes]
rs66824972	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs66899661	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs67770259	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67971141	0.89[EUR][1000 genomes]
rs71462507	0.90[EUR][1000 genomes]
rs7162983	0.81[EUR][1000 genomes]
rs7165223	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7166307	0.89[EUR][1000 genomes]
rs7169147	0.81[EUR][1000 genomes]
rs7169452	0.90[EUR][1000 genomes]
rs7170733	0.91[EUR][1000 genomes]
rs7174515	0.84[TSI][hapmap];0.90[EUR][1000 genomes]
rs7176732	0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs7176911	0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs7176935	0.90[EUR][1000 genomes]
rs7177028	0.90[EUR][1000 genomes]
rs7183236	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8025793	0.90[EUR][1000 genomes]
rs8028966	0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs8029984	0.91[EUR][1000 genomes]
rs8032004	0.91[EUR][1000 genomes]
rs8033632	0.84[TSI][hapmap];0.89[EUR][1000 genomes]
rs8033698	0.86[EUR][1000 genomes]
rs8039425	0.83[EUR][1000 genomes]
rs8039858	0.91[EUR][1000 genomes]
rs8041556	0.89[EUR][1000 genomes]
rs8042909	0.89[EUR][1000 genomes]
rs9806135	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv974620	chr15:93252874-93258773	Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93256600-93258400	Active TSS	Ovary	ovary
2	chr15:93257200-93258400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr15:93257200-93258400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr15:93257200-93258400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr15:93257200-93258400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr15:93257200-93258400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:93257200-93258400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:93257200-93258400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr15:93257200-93258400	Active TSS	Brain Hippocampus Middle	brain
10	chr15:93257200-93258400	Active TSS	Fetal Brain Female	brain
11	chr15:93257200-93258400	Active TSS	A549	lung
12	chr15:93257200-93258400	Active TSS	HSMMtube	muscle
13	chr15:93257200-93258400	Active TSS	NHDF-Ad	bronchial
14	chr15:93257200-93258400	Active TSS	NHLF	lung
15	chr15:93257400-93258400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:93257400-93258400	Active TSS	Brain Substantia Nigra	brain
17	chr15:93257400-93258400	Active TSS	Colon Smooth Muscle	Colon
18	chr15:93257400-93258400	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr15:93257400-93258400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
20	chr15:93257600-93258400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:93257600-93258400	Active TSS	iPS-20b Cell Line	embryonic stem cell
22	chr15:93257600-93258400	Active TSS	Muscle Satellite Cultured Cells	--
23	chr15:93257600-93258400	Active TSS	Brain Germinal Matrix	brain
24	chr15:93257600-93258400	Active TSS	Osteobl	bone
25	chr15:93257800-93258400	Active TSS	HUES48 Cell Line	embryonic stem cell
26	chr15:93257800-93258400	Active TSS	HUES6 Cell Line	embryonic stem cell
27	chr15:93257800-93258400	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr15:93257800-93258400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr15:93257800-93258400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
30	chr15:93257800-93258400	Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr15:93257800-93258400	Weak transcription	Fetal Heart	heart
32	chr15:93257800-93258400	Flanking Active TSS	Dnd41	blood
33	chr15:93258000-93258400	Active TSS	H1 Cell Line	embryonic stem cell
34	chr15:93258000-93258400	Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr15:93258000-93258400	Active TSS	Rectal Mucosa Donor 29	rectum
36	chr15:93258000-93258400	Active TSS	Stomach Smooth Muscle	stomach
37	chr15:93258000-93258400	Active TSS	Thymus	Thymus
38	chr15:93258000-93258800	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr15:93258200-93258400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:93258200-93258400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:93258200-93258400	Active TSS	Primary monocytes fromperipheralblood	blood
42	chr15:93258200-93258400	Enhancers	Primary B cells from cord blood	blood
43	chr15:93258200-93258400	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr15:93258200-93258400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr15:93258200-93258400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
46	chr15:93258200-93258400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
47	chr15:93258200-93258400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr15:93258200-93258400	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
49	chr15:93258200-93258400	Active TSS	Adipose Nuclei	Adipose
50	chr15:93258200-93258400	Enhancers	Liver	Liver

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