Variant report

Variant	rs28383491
Chromosome Location	chr15:59396724-59396725
allele	A/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	POLR2A	chr15:59396668-59398091	PANC-1	pancreas:	n/a	n/a
2	MXI1	chr15:59396594-59398951	SK-N-SH	brain:	n/a	n/a
3	FOXM1	chr15:59396671-59398128	SK-N-SH	brain:	n/a	n/a
4	BCLAF1	chr15:59396671-59397277	GM12878	blood:	n/a	n/a
5	ZNF384	chr15:59396710-59397432	GM12878	blood:	n/a	n/a
6	BCL3	chr15:59396624-59398316	A549	lung:	n/a	chr15:59397538-59397546 chr15:59397846-59397855 chr15:59397357-59397370
7	REST	chr15:59396650-59397580	H1-neurons	neurons:	n/a	chr15:59397337-59397344
8	ZNF384	chr15:59396631-59397527	K562	blood:	n/a	n/a
9	IRF1	chr15:59396711-59397835	K562	blood:	n/a	chr15:59397222-59397231
10	FOXM1	chr15:59396720-59398335	ECC-1	luminal epithelium:	n/a	n/a
11	E2F4	chr15:59396531-59398695	MCF10A-Er-Src	breast:	n/a	chr15:59397222-59397231
12	TBL1XR1	chr15:59396704-59397443	K562	blood:	n/a	n/a
13	PML	chr15:59396542-59397671	GM12878	blood:	n/a	n/a
14	NFYA	chr15:59396714-59397623	K562	blood:	n/a	chr15:59397220-59397234 chr15:59397253-59397268 chr15:59397255-59397265 chr15:59397220-59397235 chr15:59397253-59397271 chr15:59397253-59397268 chr15:59397253-59397267 chr15:59397220-59397235 chr15:59397219-59397231 chr15:59397222-59397232
15	CHD1	chr15:59396682-59397056	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:59277958..59282108-chr15:59396207..59399778,7	K562	blood:
2	chr15:59395795..59398698-chr15:59981439..59982956,2	K562	blood:
3	chr15:59223805..59226728-chr15:59396182..59398979,2	MCF-7	breast:
4	chr15:59391505..59393672-chr15:59394009..59396903,2	MCF-7	breast:
5	chr15:59223596..59226559-chr15:59396307..59399219,5	K562	blood:
6	chr15:59224236..59226559-chr15:59396307..59398942,5	K562	blood:
7	chr15:59396643..59397820-chr6:27100194..27101399,3	Hela-S3	cervix:

Variant related genes	Relation type
CCNB2	TF binding region
ENSG00000196787	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000157450	Chromatin interaction
ENSG00000137776	Chromatin interaction
ENSG00000140299	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11071408	0.80[ASN][1000 genomes]
rs12438949	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12441365	0.83[ASN][1000 genomes]
rs12443442	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16941030	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16941040	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16941042	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16941046	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16941051	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16941055	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16941063	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16941069	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16953412	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17236439	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044436	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2414620	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28365901	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28376133	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383490	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383497	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383502	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383504	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383512	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383513	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383514	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383519	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383520	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383523	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383531	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383536	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28383542	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383545	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383546	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383549	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383551	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383552	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383553	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28383561	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28399204	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28406885	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28491732	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28615244	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28739024	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2899643	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3751538	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3764193	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764194	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803449	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3809531	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4523870	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56187627	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56294483	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56891889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57057009	0.83[EUR][1000 genomes]
rs57750394	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57803886	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58014933	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58207484	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58321899	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58827061	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59037515	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59398329	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59921711	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60533405	0.83[EUR][1000 genomes]
rs60628647	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60785075	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61369543	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61690344	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7165934	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73418826	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73418888	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73418890	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73418896	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74017339	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74017345	0.83[EUR][1000 genomes]
rs74017356	0.86[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74017357	0.88[AFR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8035850	1.00[ASN][1000 genomes]
rs8043536	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	esv1850946	chr15:59174539-59429160	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv833025	chr15:59336148-59522176	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS 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 miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59354400-59396800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:59374000-59396800	Weak transcription	Ovary	ovary
3	chr15:59374200-59396800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr15:59374200-59396800	Weak transcription	Right Ventricle	heart
5	chr15:59374400-59396800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr15:59377200-59397000	Weak transcription	Gastric	stomach
7	chr15:59384200-59396800	Weak transcription	Lung	lung
8	chr15:59384200-59396800	Weak transcription	Pancreas	Pancrea
9	chr15:59385200-59396800	Weak transcription	Psoas Muscle	Psoas
10	chr15:59385200-59396800	Weak transcription	Small Intestine	intestine
11	chr15:59385400-59396800	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr15:59385400-59396800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr15:59385400-59396800	Weak transcription	Brain Germinal Matrix	brain
14	chr15:59385800-59396800	Weak transcription	Fetal Muscle Leg	muscle
15	chr15:59385800-59397000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:59385800-59397400	Weak transcription	Spleen	Spleen
17	chr15:59387200-59396800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:59387400-59396800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr15:59389200-59396800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:59389200-59396800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:59389200-59396800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:59389200-59396800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr15:59389200-59396800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:59389200-59396800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:59389200-59396800	Weak transcription	Colonic Mucosa	Colon
26	chr15:59389200-59396800	Weak transcription	Esophagus	oesophagus
27	chr15:59389200-59396800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:59389200-59396800	Weak transcription	Fetal Intestine Large	intestine
29	chr15:59389200-59396800	Weak transcription	Left Ventricle	heart
30	chr15:59389200-59397200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:59389600-59396800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr15:59390200-59396800	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:59390200-59396800	Weak transcription	Fetal Stomach	stomach
34	chr15:59390400-59396800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr15:59390400-59396800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:59390400-59396800	Weak transcription	Fetal Thymus	thymus
37	chr15:59390400-59396800	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr15:59390600-59396800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:59390600-59396800	Weak transcription	Fetal Intestine Small	intestine
40	chr15:59390800-59396800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr15:59391600-59396800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:59392200-59396800	Weak transcription	GM12878-XiMat	blood
43	chr15:59392600-59396800	Weak transcription	Aorta	Aorta
44	chr15:59392600-59396800	Weak transcription	Placenta	Placenta
45	chr15:59392800-59396800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr15:59392800-59396800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr15:59392800-59396800	Weak transcription	Fetal Brain Female	brain
48	chr15:59392800-59396800	Weak transcription	NH-A	brain
49	chr15:59393000-59396800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:59393000-59396800	Weak transcription	Fetal Muscle Trunk	muscle

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