Variant report

Variant	rs73462548
Chromosome Location	chr15:93258440-93258441
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	RAD21	chr15:93257813-93258529	MCF-7	breast:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996 chr15:93257849-93257863
2	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
3	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
4	RAD21	chr15:93257267-93258622	MCF-7	breast:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996 chr15:93257849-93257863
5	BRCA1	chr15:93258133-93258510	H1-hESC	embryonic stem cell:	n/a	n/a
6	RAD21	chr15:93257926-93258452	A549	lung:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996
7	ZBTB7A	chr15:93257662-93258499	ECC-1	luminal epithelium:	n/a	chr15:93258159-93258166
8	MAX	chr15:93257523-93258503	A549	lung:	n/a	n/a
9	TCF12	chr15:93257192-93258497	A549	lung:	n/a	chr15:93257767-93257774 chr15:93258112-93258122
10	CTCF	chr15:93258320-93258470	HAc	cerebellar:	n/a	n/a
11	MAX	chr15:93257167-93258509	A549	lung:	n/a	n/a
12	RFX5	chr15:93258206-93258444	H1-hESC	embryonic stem cell:	n/a	n/a
13	BCLAF1	chr15:93257946-93258444	GM12878	blood:	n/a	chr15:93258103-93258116 chr15:93257948-93257957
14	RAD21	chr15:93257856-93258496	HepG2	liver:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996
15	MAX	chr15:93257225-93258462	MCF-7	breast:	n/a	n/a
16	MYC	chr15:93258113-93258462	K562	blood:	n/a	n/a
17	SIN3AK20	chr15:93257019-93258579	MCF-7	breast:	n/a	n/a
18	CTCF	chr15:93257136-93258719	A549	lung:	n/a	chr15:93257849-93257862 chr15:93258213-93258234 chr15:93257847-93257865 chr15:93257853-93257862 chr15:93258219-93258235 chr15:93258218-93258236
19	RAD21	chr15:93257738-93258563	A549	lung:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996 chr15:93257849-93257863
20	CTCF	chr15:93257945-93258532	MCF-7	breast:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
21	CTCF	chr15:93257867-93258481	HCT-116	colon:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
22	RAD21	chr15:93257804-93258571	HCT-116	colon:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996 chr15:93257849-93257863
23	CTCF	chr15:93257871-93258471	MCF-7	breast:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
24	CTCF	chr15:93257228-93258653	SK-N-SH	brain:	n/a	chr15:93257849-93257862 chr15:93258213-93258234 chr15:93257847-93257865 chr15:93257853-93257862 chr15:93258219-93258235 chr15:93258218-93258236
25	RAD21	chr15:93257639-93258457	H1-hESC	embryonic stem cell:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996 chr15:93257849-93257863
26	RAD21	chr15:93257783-93258584	ECC-1	luminal epithelium:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996 chr15:93257849-93257863
27	RAD21	chr15:93257145-93258576	SK-N-SH	brain:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996 chr15:93257849-93257863
28	CTCF	chr15:93258027-93258484	K562	blood:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
29	E2F4	chr15:93258120-93258484	MCF10A-Er-Src	breast:	n/a	chr15:93258165-93258172 chr15:93258160-93258175 chr15:93258211-93258226
30	RAD21	chr15:93257727-93258671	IMR90	lung:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996 chr15:93257849-93257863
31	ATF3	chr15:93257797-93258453	A549	lung:	n/a	chr15:93258147-93258156
32	HDAC2	chr15:93257242-93258446	MCF-7	breast:	n/a	chr15:93257244-93257258 chr15:93257248-93257262
33	CTCF	chr15:93257960-93258445	H1-hESC	embryonic stem cell:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
34	RAD21	chr15:93257859-93258472	HCT-116	colon:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996
35	RAD21	chr15:93257932-93258494	ECC-1	luminal epithelium:	n/a	chr15:93258216-93258235 chr15:93258222-93258231 chr15:93257982-93257996
36	E2F6	chr15:93257412-93258444	A549	lung:	n/a	chr15:93257842-93257854 chr15:93258165-93258172 chr15:93258160-93258175 chr15:93258112-93258122 chr15:93258211-93258226
37	CTCF	chr15:93257675-93258448	GM12878	blood:	n/a	chr15:93257849-93257862 chr15:93258213-93258234 chr15:93257847-93257865 chr15:93257853-93257862 chr15:93258219-93258235 chr15:93258218-93258236
38	CTCF	chr15:93257866-93258572	HCT-116	colon:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
39	CTCF	chr15:93257907-93258465	A549	lung:	n/a	chr15:93258213-93258234 chr15:93258219-93258235 chr15:93258218-93258236
40	REST	chr15:93257029-93258503	H1-neurons	neurons:	n/a	n/a
41	SMC3	chr15:93257221-93258492	SK-N-SH	brain:	n/a	chr15:93257849-93257863 chr15:93257849-93257859 chr15:93258220-93258234

No.	Distal block	Cell Line	Cell type
1	chr15:93237040..93237940-chr15:93257791..93258641,4	MCF-7	breast:
2	chr15:93258240..93259897-chr15:93272535..93274240,2	MCF-7	breast:
3	chr15:93237881..93239746-chr15:93257502..93259973,2	MCF-7	breast:
4	chr15:93191617..93195403-chr15:93257490..93261490,4	MCF-7	breast:
5	chr15:92640503..92641006-chr15:93257734..93258635,2	K562	blood:
6	chr15:93195935..93200377-chr15:93256556..93260471,5	MCF-7	breast:
7	chr15:93226419..93227336-chr15:93257734..93258779,3	MCF-7	breast:
8	chr15:93252649..93254753-chr15:93257319..93260184,2	MCF-7	breast:
9	chr15:93064480..93065790-chr15:93258050..93258792,4	MCF-7	breast:
10	chr15:93064431..93065465-chr15:93257828..93258686,4	MCF-7	breast:
11	chr15:93187273..93189424-chr15:93256884..93259260,2	MCF-7	breast:
12	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: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs16947186	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1814416	1.00[ASN][1000 genomes]
rs2388020	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2388021	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55681576	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55839405	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57193023	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58217777	1.00[ASN][1000 genomes]
rs59813575	1.00[ASN][1000 genomes]
rs60612764	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60831032	1.00[ASN][1000 genomes]
rs66985158	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67027103	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67982358	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167997	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172949	1.00[ASN][1000 genomes]
rs7178841	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73450624	1.00[ASN][1000 genomes]
rs73450627	1.00[ASN][1000 genomes]
rs8024790	1.00[ASN][1000 genomes]
rs8025959	1.00[ASN][1000 genomes]
rs8026417	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8039403	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs934784	1.00[ASN][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:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93258000-93258800	Enhancers	Primary T helper naive cells from peripheral blood	blood
2	chr15:93258200-93258600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:93258200-93258600	Enhancers	Primary neutrophils fromperipheralblood	blood
4	chr15:93258200-93258600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:93258200-93258600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
6	chr15:93258200-93258600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr15:93258200-93258600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr15:93258200-93258600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:93258200-93258600	Enhancers	Brain Angular Gyrus	brain
10	chr15:93258200-93258600	Flanking Active TSS	Brain Anterior Caudate	brain
11	chr15:93258200-93258600	Enhancers	Brain Cingulate Gyrus	brain
12	chr15:93258200-93258600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:93258200-93258600	Enhancers	Fetal Intestine Large	intestine
14	chr15:93258200-93258600	Flanking Active TSS	Rectal Smooth Muscle	rectum
15	chr15:93258200-93258600	Bivalent Enhancer	HepG2	liver
16	chr15:93258200-93258600	Enhancers	HSMM	muscle
17	chr15:93258200-93258800	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr15:93258200-93258800	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr15:93258200-93258800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr15:93258200-93258800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
21	chr15:93258200-93258800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:93258200-93258800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr15:93258200-93258800	Enhancers	Fetal Brain Male	brain
24	chr15:93258200-93259000	Enhancers	Fetal Kidney	kidney
25	chr15:93258200-93259000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr15:93258200-93259200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:93258200-93259200	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr15:93258200-93259800	Enhancers	Fetal Stomach	stomach
29	chr15:93258200-93260000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr15:93258200-93260200	Enhancers	Fetal Lung	lung
31	chr15:93258200-93261000	Weak transcription	Right Atrium	heart
32	chr15:93258200-93277000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr15:93258200-93277000	Weak transcription	Left Ventricle	heart
34	chr15:93258400-93258600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr15:93258400-93258600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
36	chr15:93258400-93258600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr15:93258400-93258600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr15:93258400-93258600	Bivalent Enhancer	Primary B cells from cord blood	blood
39	chr15:93258400-93258600	Enhancers	Primary T cells from cord blood	blood
40	chr15:93258400-93258600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
41	chr15:93258400-93258600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
42	chr15:93258400-93258600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:93258400-93258600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr15:93258400-93258600	Enhancers	Brain Hippocampus Middle	brain
45	chr15:93258400-93258600	Weak transcription	Brain Substantia Nigra	brain
46	chr15:93258400-93258600	Flanking Active TSS	Colon Smooth Muscle	Colon
47	chr15:93258400-93258600	Enhancers	Fetal Heart	heart
48	chr15:93258400-93258600	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr15:93258400-93258600	Enhancers	A549	lung
50	chr15:93258400-93258600	Enhancers	Dnd41	blood

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