Variant report

Variant	rs555761680
Chromosome Location	chr15:52310918-52310919
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	SMARCC1	chr15:52310695-52311541	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr15:52310865-52311810	U87	brain:	n/a	n/a
3	POLR2A	chr15:52310872-52311769	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:52310700-52313695	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:52310849-52312297	Raji	blood:	n/a	n/a
6	POLR2A	chr15:52310853-52312523	K562	blood:	n/a	n/a
7	NFYA	chr15:52310898-52311453	Hela-S3	cervix:	n/a	n/a
8	REST	chr15:52310736-52312948	H1-neurons	neurons:	n/a	chr15:52311953-52311966
9	TAF1	chr15:52310910-52311797	MCF-7	breast:	n/a	n/a
10	PML	chr15:52310843-52311662	K562	blood:	n/a	n/a
11	NFIC	chr15:52310905-52311598	GM12878	blood:	n/a	n/a
12	POLR2A	chr15:52310863-52311717	K562	blood:	n/a	n/a
13	POLR2A	chr15:52310883-52311797	SK-N-MC	brain:	n/a	n/a
14	POLR2A	chr15:52310834-52312878	GM12878	blood:	n/a	n/a
15	TBP	chr15:52310893-52311670	H1-hESC	embryonic stem cell:	n/a	n/a
16	SP1	chr15:52310883-52311772	A549	lung:	n/a	chr15:52311385-52311395 chr15:52311385-52311395 chr15:52311404-52311414 chr15:52311404-52311413 chr15:52311404-52311414 chr15:52311340-52311352 chr15:52311403-52311415 chr15:52311410-52311424 chr15:52311405-52311414 chr15:52311404-52311418 chr15:52311346-52311357 chr15:52311404-52311413 chr15:52311403-52311415 chr15:52311347-52311356
17	MTA3	chr15:52310826-52311614	GM12878	blood:	n/a	n/a
18	GATA3	chr15:52310883-52312485	MCF-7	breast:	n/a	chr15:52312122-52312129
19	MAX	chr15:52310847-52311663	K562	blood:	n/a	chr15:52311406-52311416 chr15:52311341-52311351
20	POLR2A	chr15:52310709-52311693	GM12878	blood:	n/a	n/a
21	MAX	chr15:52310918-52311612	NB4	blood:	n/a	chr15:52311406-52311416 chr15:52311341-52311351
22	MXI1	chr15:52310700-52314090	SK-N-SH	brain:	n/a	n/a
23	CREB1	chr15:52310916-52311657	HepG2	liver:	n/a	n/a
24	POLR2A	chr15:52310908-52311783	HUVEC	blood vessel:	n/a	n/a
25	ZKSCAN1	chr15:52310606-52311627	Hela-S3	cervix:	n/a	n/a
26	CHD1	chr15:52310864-52311657	GM12878	blood:	n/a	n/a
27	POLR2A	chr15:52310902-52312332	HL-60	blood:	n/a	n/a
28	POLR2A	chr15:52310793-52312427	ProgFib	skin:	n/a	n/a
29	E2F6	chr15:52310789-52311650	A549	lung:	n/a	chr15:52311347-52311359 chr15:52311405-52311414 chr15:52311459-52311467
30	NR2F2	chr15:52310906-52311543	K562	blood:	n/a	n/a
31	POLR2A	chr15:52310908-52311601	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAX	chr15:52310663-52312582	MCF-7	breast:	n/a	chr15:52311406-52311416 chr15:52311341-52311351
33	HA-E2F1	chr15:52310813-52311619	MCF-7	breast:	n/a	chr15:52311347-52311359 chr15:52311405-52311414 chr15:52311347-52311358
34	SIN3AK20	chr15:52310743-52313038	MCF-7	breast:	n/a	n/a
35	TEAD4	chr15:52310916-52311644	ECC-1	luminal epithelium:	n/a	n/a
36	PBX3	chr15:52310820-52311660	A549	lung:	n/a	n/a
37	BHLHE40	chr15:52310814-52311605	A549	lung:	n/a	chr15:52311478-52311494
38	POLR2A	chr15:52310802-52312396	HL-60	blood:	n/a	n/a
39	MAX	chr15:52310856-52312590	HepG2	liver:	n/a	chr15:52311406-52311416 chr15:52311341-52311351
40	CHD2	chr15:52310842-52312689	Hela-S3	cervix:	n/a	n/a
41	RELA	chr15:52310900-52311693	GM15510	blood:	n/a	chr15:52311311-52311320 chr15:52311311-52311320
42	RCOR1	chr15:52310733-52311584	K562	blood:	n/a	n/a
43	E2F6	chr15:52310847-52312299	K562	blood:	n/a	chr15:52311347-52311359 chr15:52311405-52311414 chr15:52311704-52311714 chr15:52311918-52311928 chr15:52311906-52311915 chr15:52311459-52311467 chr15:52312011-52312021
44	POLR2A	chr15:52310587-52313959	MCF10A-Er-Src	breast:	n/a	n/a
45	MAZ	chr15:52310867-52312357	K562	blood:	n/a	chr15:52311406-52311416 chr15:52311341-52311351
46	TAF1	chr15:52310752-52311771	A549	lung:	n/a	n/a
47	RUNX3	chr15:52310905-52311600	GM12878	blood:	n/a	n/a
48	POLR2A	chr15:52310681-52311613	K562	blood:	n/a	n/a
49	MAX	chr15:52310868-52312287	ECC-1	luminal epithelium:	n/a	chr15:52311406-52311416 chr15:52311341-52311351
50	MAX	chr15:52310775-52312362	HCT-116	colon:	n/a	chr15:52311406-52311416 chr15:52311341-52311351

No.	Distal block	Cell Line	Cell type
1	chr15:52310752..52311563-chr15:80215677..80216555,2	Hela-S3	cervix:
2	chr15:52309643..52312109-chr15:52424380..52429568,4	MCF-7	breast:
3	chr15:52310228..52314421-chr15:52470196..52474583,10	MCF-7	breast:
4	chr15:51914606..51918105-chr15:52309438..52311518,3	K562	blood:
5	chr15:52309956..52312123-chr15:52404856..52406463,2	MCF-7	breast:
6	chr15:52310337..52312699-chr15:76160460..76162429,2	MCF-7	breast:
7	chr15:52259207..52267788-chr15:52308373..52314434,24	MCF-7	breast:
8	chr15:52310908..52311894-chr6:26158225..26159035,2	Hela-S3	cervix:
9	chr15:52308069..52314807-chr15:52359242..52376066,34	MCF-7	breast:
10	chr15:52262145..52266701-chr15:52309209..52314377,19	MCF-7	breast:
11	chr1:149857624..149859887-chr15:52308865..52312483,3	MCF-7	breast:
12	chr15:51913842..51915651-chr15:52310480..52312908,3	MCF-7	breast:
13	chr15:52262263..52265564-chr15:52309489..52315686,9	K562	blood:
14	chr15:52309759..52313480-chr15:52429073..52432426,3	K562	blood:
15	chr1:150551175..150551879-chr15:52310855..52311822,2	Hela-S3	cervix:
16	chr15:52262270..52265607-chr15:52309730..52314612,10	K562	blood:
17	chr13:113861573..113863819-chr15:52310834..52313167,2	MCF-7	breast:
18	chr15:52309194..52314432-chr15:52385325..52393461,10	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LEO1-3	chr15:52310896-52311292	ENSG00000259438.1

Variant related genes	Relation type
MAPK6	TF binding region
ENSG00000259178	Chromatin interaction
ENSG00000259709	Chromatin interaction
ENSG00000259577	Chromatin interaction
ENSG00000180953	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000069966	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000242327	Chromatin interaction
ENSG00000104093	Chromatin interaction
ENSG00000166477	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000140367	Chromatin interaction
ENSG00000139842	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000259712	Chromatin interaction
ENSG00000137875	Chromatin interaction
ENSG00000259332	Chromatin interaction
ENSG00000143384	Chromatin interaction
ENSG00000126226	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

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	nsv1047260	chr15:52257100-52337418	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
2	nsv1050664	chr15:52265723-52342101	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv1536	chr15:52276293-52320919	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv530681	chr15:52297253-52390470	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
6	esv3330502	chr15:52310485-52313033	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52309800-52311000	Enhancers	Placenta Amnion	Placenta Amnion
2	chr15:52310400-52311400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr15:52310600-52311000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
4	chr15:52310600-52311000	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr15:52310600-52311200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:52310600-52311200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr15:52310600-52311200	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr15:52310600-52311200	Flanking Active TSS	Fetal Brain Male	brain
9	chr15:52310600-52311200	Flanking Active TSS	GM12878-XiMat	blood
10	chr15:52310600-52311200	Flanking Active TSS	Hela-S3	cervix
11	chr15:52310600-52311200	Flanking Active TSS	HepG2	liver
12	chr15:52310600-52311200	Flanking Active TSS	K562	blood
13	chr15:52310600-52311400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:52310600-52311400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr15:52310600-52313200	Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr15:52310600-52313800	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr15:52310600-52313800	Active TSS	H1 Cell Line	embryonic stem cell
18	chr15:52310600-52313800	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr15:52310800-52311000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:52310800-52311000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:52310800-52311000	Flanking Active TSS	H9 Cell Line	embryonic stem cell
22	chr15:52310800-52311000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:52310800-52311000	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
24	chr15:52310800-52311000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr15:52310800-52311000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr15:52310800-52311000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:52310800-52311000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
28	chr15:52310800-52311000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
29	chr15:52310800-52311000	Enhancers	Esophagus	oesophagus
30	chr15:52310800-52311000	Weak transcription	Fetal Heart	heart
31	chr15:52310800-52311000	Enhancers	Fetal Intestine Large	intestine
32	chr15:52310800-52311000	Enhancers	Fetal Lung	lung
33	chr15:52310800-52311000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
34	chr15:52310800-52311000	Enhancers	Fetal Thymus	thymus
35	chr15:52310800-52311000	Enhancers	Left Ventricle	heart
36	chr15:52310800-52311000	Enhancers	Lung	lung
37	chr15:52310800-52311000	Enhancers	Pancreas	Pancrea
38	chr15:52310800-52311000	Enhancers	Right Atrium	heart
39	chr15:52310800-52311000	Enhancers	Right Ventricle	heart
40	chr15:52310800-52311000	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr15:52310800-52311000	Enhancers	Spleen	Spleen
42	chr15:52310800-52311200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr15:52310800-52311200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:52310800-52311200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:52310800-52311200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr15:52310800-52311200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr15:52310800-52311200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr15:52310800-52311200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr15:52310800-52311200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
50	chr15:52310800-52311200	Flanking Active TSS	Primary B cells from cord blood	blood

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