Variant report

Variant	rs56818859
Chromosome Location	chr15:78833462-78833463
allele	A/C
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	JUND	chr15:78832441-78833558	K562	blood:	n/a	chr15:78832738-78832747
2	GATA2	chr15:78832738-78833831	SH-SY5Y	brain:	n/a	n/a
3	MAX	chr15:78832479-78833520	SK-N-SH	brain:	n/a	chr15:78833105-78833115 chr15:78833118-78833128
4	MXI1	chr15:78832315-78833620	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:78832284-78834051	K562	blood:	n/a	n/a
6	STAT3	chr15:78833299-78833499	MCF10A-Er-Src	breast:	n/a	n/a
7	NFYA	chr15:78833216-78833675	Hela-S3	cervix:	n/a	n/a
8	NFYB	chr15:78833118-78833743	Hela-S3	cervix:	n/a	chr15:78833462-78833477
9	POLR2A	chr15:78830840-78834174	GM12878	blood:	n/a	n/a
10	POLR2A	chr15:78832400-78833576	NB4	blood:	n/a	n/a
11	MYC	chr15:78832270-78833718	K562	blood:	n/a	chr15:78833105-78833115 chr15:78833118-78833128
12	TAF1	chr15:78832251-78833566	A549	lung:	n/a	n/a
13	POLR2A	chr15:78832174-78833462	GM12892	blood:	n/a	n/a
14	POLR2A	chr15:78832398-78833473	H1-hESC	embryonic stem cell:	n/a	n/a
15	RELA	chr15:78832408-78833971	GM18951	blood:	n/a	n/a
16	RFX5	chr15:78832303-78834452	Hela-S3	cervix:	n/a	chr15:78833791-78833799
17	POLR2A	chr15:78832230-78834004	GM18951	blood:	n/a	n/a
18	NFYB	chr15:78833261-78833690	GM12878	blood:	n/a	chr15:78833462-78833477
19	POLR2A	chr15:78832316-78834361	K562	blood:	n/a	n/a
20	SMC3	chr15:78833177-78833688	GM12878	blood:	n/a	n/a
21	POLR2A	chr15:78831151-78834112	GM12878	blood:	n/a	n/a
22	USF2	chr15:78833283-78833509	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr15:78832447-78833507	ECC-1	luminal epithelium:	n/a	n/a
24	RFX5	chr15:78833420-78833580	GM12878	blood:	n/a	n/a
25	CEBPB	chr15:78832334-78834434	Hela-S3	cervix:	n/a	chr15:78833564-78833576 chr15:78833563-78833576 chr15:78833592-78833604
26	TCF12	chr15:78832185-78833782	A549	lung:	n/a	n/a
27	POLR2A	chr15:78832166-78833767	GM19193	blood:	n/a	n/a
28	MAZ	chr15:78832418-78834342	IMR90	lung:	n/a	chr15:78833105-78833115 chr15:78833118-78833128 chr15:78833991-78834000
29	POLR2A	chr15:78830693-78835554	GM12891	blood:	n/a	n/a
30	NFYA	chr15:78833291-78833540	GM12878	blood:	n/a	n/a
31	POLR2A	chr15:78832436-78833512	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr15:78832165-78833847	A549	lung:	n/a	chr15:78833105-78833115 chr15:78833118-78833128
33	PML	chr15:78832237-78833899	GM12878	blood:	n/a	n/a
34	POLR2A	chr15:78832147-78834182	GM18505	blood:	n/a	n/a
35	POLR2A	chr15:78831504-78834721	MCF10A-Er-Src	breast:	n/a	n/a
36	POLR2A	chr15:78831753-78833808	GM12892	blood:	n/a	n/a
37	GTF2F1	chr15:78832402-78834161	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr15:78832392-78834179	GM12878	blood:	n/a	n/a
39	GATA3	chr15:78833454-78833853	T-47D	breast:	n/a	n/a
40	POLR2A	chr15:78832151-78833492	GM12891	blood:	n/a	n/a
41	POLR2A	chr15:78832311-78834043	IMR90	lung:	n/a	n/a
42	POLR2A	chr15:78832172-78833750	K562	blood:	n/a	n/a
43	POLR2A	chr15:78832262-78833759	Hela-S3	cervix:	n/a	n/a
44	RELA	chr15:78832430-78833990	GM12891	blood:	n/a	n/a
45	NFYB	chr15:78833265-78833632	K562	blood:	n/a	chr15:78833462-78833477
46	POLR2A	chr15:78831941-78833534	GM12891	blood:	n/a	n/a
47	POLR2A	chr15:78832199-78833477	U87	brain:	n/a	n/a
48	POLR2A	chr15:78831936-78833626	GM12892	blood:	n/a	n/a
49	POLR2A	chr15:78832188-78833615	GM15510	blood:	n/a	n/a
50	POLR2A	chr15:78832371-78833958	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:78831297..78836398-chr15:78856605..78860226,12	MCF-7	breast:
2	chr15:78832604..78836535-chr15:78856473..78859290,6	MCF-7	breast:
3	chr15:78797464..78804546-chr15:78829529..78835433,12	MCF-7	breast:
4	chr15:78832891..78834488-chr15:78856612..78858995,2	K562	blood:
5	chr15:78576883..78578539-chr15:78832474..78833981,2	MCF-7	breast:
6	chr15:78831312..78834277-chr15:78872379..78875019,2	MCF-7	breast:
7	chr15:78798844..78801827-chr15:78830907..78834394,5	MCF-7	breast:
8	chr15:78831864..78834406-chr17:59476584..59478636,2	MCF-7	breast:
9	chr15:78556899..78558870-chr15:78832501..78834304,2	MCF-7	breast:
10	chr15:78829726..78834442-chr15:78855710..78860360,8	K562	blood:
11	chr15:78729933..78731610-chr15:78832734..78835693,2	MCF-7	breast:

Variant related genes	Relation type
PSMA4	TF binding region
ENSG00000121068	Chromatin interaction
ENSG00000140403	Chromatin interaction
ENSG00000140395	Chromatin interaction
ENSG00000169684	Chromatin interaction
ENSG00000136381	Chromatin interaction
ENSG00000267131	Chromatin interaction
ENSG00000188266	Chromatin interaction
ENSG00000267280	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16969914	1.00[AMR][1000 genomes]
rs57996982	1.00[AMR][1000 genomes]
rs59737941	1.00[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59778788	1.00[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs60958974	1.00[AMR][1000 genomes]
rs71537686	1.00[AMR][1000 genomes]
rs71541945	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1038816	chr15:78796434-78881087	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	48 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	chr15:78832000-78833800	Active TSS	Colon Smooth Muscle	Colon
2	chr15:78832000-78834200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr15:78832000-78834200	Active TSS	Duodenum Mucosa	Duodenum
4	chr15:78832000-78834600	Active TSS	Colonic Mucosa	Colon
5	chr15:78832200-78833600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr15:78832200-78833600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
7	chr15:78832200-78833600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:78832200-78833600	Active TSS	Brain Angular Gyrus	brain
9	chr15:78832200-78833600	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr15:78832200-78833600	Active TSS	Brain Substantia Nigra	brain
11	chr15:78832200-78833600	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr15:78832200-78833600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
13	chr15:78832200-78833600	Active TSS	Fetal Brain Female	brain
14	chr15:78832200-78833600	Active TSS	Fetal Stomach	stomach
15	chr15:78832200-78833600	Active TSS	Spleen	Spleen
16	chr15:78832200-78833600	Active TSS	HUVEC	blood vessel
17	chr15:78832200-78833800	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr15:78832200-78833800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr15:78832200-78833800	Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr15:78832200-78833800	Active TSS	Muscle Satellite Cultured Cells	--
21	chr15:78832200-78833800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:78832200-78833800	Active TSS	Fetal Intestine Small	intestine
23	chr15:78832200-78833800	Active TSS	Gastric	stomach
24	chr15:78832200-78833800	Active TSS	Rectal Smooth Muscle	rectum
25	chr15:78832200-78833800	Active TSS	Hela-S3	cervix
26	chr15:78832200-78834000	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr15:78832200-78834000	Active TSS	H1 Cell Line	embryonic stem cell
28	chr15:78832200-78834000	Active TSS	iPS-18 Cell Line	embryonic stem cell
29	chr15:78832200-78834000	Active TSS	Primary T killer memory cells from peripheral blood	blood
30	chr15:78832200-78834000	Active TSS	Fetal Intestine Large	intestine
31	chr15:78832200-78834000	Active TSS	Fetal Kidney	kidney
32	chr15:78832200-78834000	Active TSS	Placenta	Placenta
33	chr15:78832200-78834000	Active TSS	Left Ventricle	heart
34	chr15:78832200-78834000	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr15:78832200-78834000	Active TSS	Right Ventricle	heart
36	chr15:78832200-78834000	Active TSS	Stomach Mucosa	stomach
37	chr15:78832200-78834000	Active TSS	A549	lung
38	chr15:78832200-78834000	Active TSS	HMEC	breast
39	chr15:78832200-78834000	Active TSS	NHDF-Ad	bronchial
40	chr15:78832200-78834200	Active TSS	H9 Cell Line	embryonic stem cell
41	chr15:78832200-78834200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:78832200-78834200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr15:78832200-78834200	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr15:78832200-78834200	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr15:78832200-78834200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:78832200-78834200	Active TSS	iPS-15b Cell Line	embryonic stem cell
47	chr15:78832200-78834200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:78832200-78834200	Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr15:78832200-78834200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:78832200-78834200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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