Variant report

Variant	rs8552
Chromosome Location	chr15:50646783-50646784
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	HA-E2F1	chr15:50646148-50648061	MCF-7	breast:	n/a	chr15:50646909-50646919 chr15:50647327-50647342 chr15:50647651-50647660 chr15:50647024-50647034 chr15:50646749-50646759 chr15:50646768-50646780 chr15:50647648-50647658
2	TCF7L2	chr15:50646105-50647882	HCT-116	colon:	n/a	chr15:50646167-50646174
3	POLR2A	chr15:50646680-50648025	GM12878	blood:	n/a	n/a
4	REST	chr15:50646057-50648064	MCF-7	breast:	n/a	n/a
5	POLR2A	chr15:50646114-50648058	GM10847	blood:	n/a	n/a
6	TCF12	chr15:50645904-50648268	A549	lung:	n/a	n/a
7	POLR2A	chr15:50646558-50648021	ECC-1	luminal epithelium:	n/a	n/a
8	GATA3	chr15:50645961-50648246	MCF-7	breast:	n/a	chr15:50646826-50646835 chr15:50647396-50647405
9	YY1	chr15:50646641-50647974	GM12878	blood:	n/a	chr15:50646905-50646919 chr15:50646908-50646917 chr15:50646911-50646920 chr15:50646691-50646705
10	YY1	chr15:50646216-50648020	K562	blood:	n/a	chr15:50646905-50646919 chr15:50646908-50646917 chr15:50646911-50646920 chr15:50646519-50646528 chr15:50646691-50646705
11	ETS1	chr15:50646652-50647919	GM12878	blood:	n/a	chr15:50647627-50647640 chr15:50647090-50647106 chr15:50646906-50646917 chr15:50647140-50647149 chr15:50647140-50647149 chr15:50647140-50647149 chr15:50647140-50647149
12	MAX	chr15:50646622-50648126	ECC-1	luminal epithelium:	n/a	chr15:50646903-50646913 chr15:50647687-50647697
13	FOXP2	chr15:50646578-50647502	PFSK-1	brain:	n/a	n/a
14	MAX	chr15:50646521-50648042	H1-hESC	embryonic stem cell:	n/a	chr15:50646903-50646913 chr15:50647687-50647697
15	POLR2A	chr15:50645890-50649461	GM18505	blood:	n/a	n/a
16	MXI1	chr15:50645398-50648299	GM12878	blood:	n/a	n/a
17	HCFC1	chr15:50646685-50647971	K562	blood:	n/a	n/a
18	POLR2A	chr15:50646107-50648067	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTBP2	chr15:50646254-50647790	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr15:50646024-50648000	K562	blood:	n/a	n/a
21	SPI1	chr15:50646618-50646812	K562	blood:	n/a	chr15:50646760-50646767 chr15:50646758-50646771
22	POLR2A	chr15:50646141-50647951	K562	blood:	n/a	n/a
23	CHD2	chr15:50646653-50648035	K562	blood:	n/a	chr15:50647640-50647650 chr15:50646931-50646941
24	HEY1	chr15:50646036-50648145	K562	blood:	n/a	chr15:50647646-50647661 chr15:50647255-50647270 chr15:50647648-50647663 chr15:50646538-50646553
25	POLR2A	chr15:50646131-50648005	A549	lung:	n/a	n/a
26	TBP	chr15:50646128-50648097	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr15:50646718-50648031	Gliobla	brain:	n/a	n/a
28	EBF1	chr15:50646654-50647104	GM12878	blood:	n/a	n/a
29	RCOR1	chr15:50646765-50647967	GM12878	blood:	n/a	n/a
30	POLR2A	chr15:50643941-50650733	GM12891	blood:	n/a	n/a
31	MAX	chr15:50646726-50648030	GM12878	blood:	n/a	chr15:50646903-50646913 chr15:50647687-50647697
32	POLR2A	chr15:50645980-50648085	GM19193	blood:	n/a	n/a
33	POLR2A	chr15:50646568-50648024	H1-hESC	embryonic stem cell:	n/a	n/a
34	STAT5A	chr15:50646603-50648075	GM12878	blood:	n/a	chr15:50647305-50647325
35	ETS1	chr15:50646422-50647863	K562	blood:	n/a	chr15:50647627-50647640 chr15:50647090-50647106 chr15:50646509-50646522 chr15:50646906-50646917 chr15:50647140-50647149 chr15:50647140-50647149 chr15:50647140-50647149 chr15:50647140-50647149
36	SIN3AK20	chr15:50645321-50648400	MCF-7	breast:	n/a	n/a
37	POLR2A	chr15:50645476-50650223	GM12878	blood:	n/a	n/a
38	FOSL2	chr15:50646119-50648169	MCF-7	breast:	n/a	chr15:50647394-50647405
39	POLR2A	chr15:50646011-50648183	K562	blood:	n/a	n/a
40	CHD2	chr15:50646061-50648049	Hela-S3	cervix:	n/a	chr15:50647640-50647650 chr15:50646931-50646941
41	POLR2A	chr15:50646173-50648030	A549	lung:	n/a	n/a
42	POLR2A	chr15:50645482-50648214	HUVEC	blood vessel:	n/a	n/a
43	MAX	chr15:50645921-50648376	A549	lung:	n/a	chr15:50646903-50646913 chr15:50647687-50647697
44	TCF3	chr15:50646652-50647843	GM12878	blood:	n/a	n/a
45	POLR2A	chr15:50646743-50648506	PFSK-1	brain:	n/a	n/a
46	RELA	chr15:50646059-50648088	GM18951	blood:	n/a	n/a
47	TAF1	chr15:50646192-50648094	ECC-1	luminal epithelium:	n/a	n/a
48	RUNX3	chr15:50645366-50648103	GM12878	blood:	n/a	n/a
49	ZBTB7A	chr15:50646621-50647468	K562	blood:	n/a	n/a
50	POLR2A	chr15:50645817-50648434	GM18526	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:50645594..50649830-chr15:50754186..50757976,9	MCF-7	breast:
2	chr15:50645825..50647611-chr17:74731660..74734428,2	MCF-7	breast:
3	chr15:50646435..50649191-chr15:52859384..52862079,2	MCF-7	breast:
4	chr15:50646735..50647719-chr2:47403564..47404098,2	Hela-S3	cervix:
5	chr15:50473235..50476211-chr15:50645559..50648841,7	MCF-7	breast:
6	chr15:50619147..50621799-chr15:50645712..50648185,2	K562	blood:
7	chr15:50645577..50647649-chr15:52968775..52972037,3	MCF-7	breast:
8	chr15:50626190..50628590-chr15:50644878..50647034,2	K562	blood:
9	chr15:50645819..50647987-chr15:50977616..50981646,3	MCF-7	breast:
10	chr15:50643783..50647096-chr15:50681349..50683673,3	K562	blood:
11	chr1:149856230..149858329-chr15:50645026..50647527,2	MCF-7	breast:
12	chr15:50643045..50650563-chr15:50756489..50761004,9	MCF-7	breast:
13	chr10:112257094..112257617-chr15:50646519..50647398,2	NB4	blood:
14	chr15:50644767..50646940-chr15:50764090..50766504,2	MCF-7	breast:
15	chr15:49446244..49450190-chr15:50645448..50647621,4	K562	blood:
16	chr15:50471646..50476620-chr15:50646050..50650091,9	MCF-7	breast:
17	chr15:50646061..50647679-chr17:57970220..57971853,2	MCF-7	breast:
18	chr15:50601193..50602904-chr15:50644930..50647260,2	MCF-7	breast:
19	chr11:62656488..62658852-chr15:50644202..50647028,2	K562	blood:
20	chr15:50410321..50412713-chr15:50646391..50648447,2	MCF-7	breast:
21	chr15:50644389..50649393-chr15:50787180..50791359,7	MCF-7	breast:
22	chr15:50646264..50649073-chr17:62500886..62503658,2	MCF-7	breast:
23	chr15:50645553..50650972-chr15:51199033..51203961,11	MCF-7	breast:
24	chr15:50646295..50648191-chr17:56159930..56162089,2	MCF-7	breast:
25	chr15:50513432..50516110-chr15:50646563..50649335,2	MCF-7	breast:
26	chr15:50646256..50647079-chr5:90676975..90677756,2	HCT-116	colon:
27	chr15:50646294..50648601-chr15:50837515..50839531,2	MCF-7	breast:
28	chr15:50552898..50556236-chr15:50646166..50649137,4	K562	blood:
29	chr15:50644593..50647982-chr15:50708471..50714039,7	MCF-7	breast:
30	chr15:50645500..50647866-chr17:56706889..56709472,3	MCF-7	breast:
31	chr1:234614349..234616741-chr15:50645455..50648119,2	MCF-7	breast:
32	chr15:50645564..50647372-chr15:50783247..50786142,2	MCF-7	breast:
33	chr11:66486776..66489307-chr15:50646648..50649417,2	MCF-7	breast:
34	chr15:50644809..50652796-chr15:50713240..50720627,20	K562	blood:
35	chr12:108078496..108080358-chr15:50646042..50648645,2	MCF-7	breast:
36	chr15:50356816..50359493-chr15:50643389..50647117,3	MCF-7	breast:
37	chr15:50646678..50647430-chr19:50320490..50321438,2	Hela-S3	cervix:
38	chr15:50646198..50649019-chr15:50789771..50791870,3	MCF-7	breast:
39	chr15:49913123..49914709-chr15:50646540..50648629,2	K562	blood:
40	chr15:50646161..50647071-chr17:43225786..43226351,2	Hela-S3	cervix:
41	chr15:50645588..50649349-chr15:50728196..50732461,4	MCF-7	breast:
42	chr15:50646468..50650762-chr15:50786083..50789645,4	K562	blood:
43	chr15:50646263..50647220-chr17:48784225..48784847,2	Hela-S3	cervix:
44	chr12:53846173..53846818-chr15:50646342..50647257,2	Hela-S3	cervix:
45	chr15:50646379..50648105-chr15:52310964..52313763,2	MCF-7	breast:
46	chr15:50644661..50647207-chr15:51058214..51061180,2	MCF-7	breast:
47	chr15:50646359..50649336-chr15:50872616..50874692,3	MCF-7	breast:
48	chr15:50644978..50654282-chr15:50714279..50723145,48	MCF-7	breast:
49	chr15:50646133..50648665-chr7:100026247..100027987,2	MCF-7	breast:
50	chr15:50646583..50647294-chr19:8509555..8510201,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HDC-2	chr15:50646075-50647070	NONHSAT042403
2	lnc-HDC-2	chr15:50641135-50647076	NONHSAT042404
3	lnc-USP8-2	chr15:50646371-50650503	NONHSAT042406

Variant related genes	Relation type
GABPB1-AS1	TF binding region
ENSG00000069956	Chromatin interaction
ENSG00000141232	Chromatin interaction
ENSG00000136045	Chromatin interaction
ENSG00000259465	Chromatin interaction
ENSG00000259438	Chromatin interaction
ENSG00000166262	Chromatin interaction
ENSG00000173898	Chromatin interaction
ENSG00000099783	Chromatin interaction
ENSG00000156958	Chromatin interaction
ENSG00000092931	Chromatin interaction
ENSG00000140284	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000138592	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000259298	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000136997	Chromatin interaction
ENSG00000242737	Chromatin interaction
ENSG00000059588	Chromatin interaction
ENSG00000143933	Chromatin interaction
ENSG00000229980	Chromatin interaction
ENSG00000128989	Chromatin interaction
ENSG00000259618	Chromatin interaction
ENSG00000104043	Chromatin interaction
ENSG00000092439	Chromatin interaction
ENSG00000010361	Chromatin interaction
ENSG00000065361	Chromatin interaction
ENSG00000108423	Chromatin interaction
ENSG00000170236	Chromatin interaction
ENSG00000047346	Chromatin interaction
ENSG00000108654	Chromatin interaction
ENSG00000266290	Chromatin interaction
ENSG00000243027	Chromatin interaction
ENSG00000161547	Chromatin interaction
ENSG00000140287	Chromatin interaction
ENSG00000081014	Chromatin interaction
ENSG00000104047	Chromatin interaction
ENSG00000166200	Chromatin interaction
ENSG00000131149	Chromatin interaction
ENSG00000207556	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000091651	Chromatin interaction
ENSG00000197111	Chromatin interaction
ENSG00000108443	Chromatin interaction
ENSG00000184678	Chromatin interaction
ENSG00000252376	Chromatin interaction
ENSG00000138166	Chromatin interaction
ENSG00000258890	Chromatin interaction
ENSG00000168502	Chromatin interaction
ENSG00000264364	Chromatin interaction
ENSG00000200605	Chromatin interaction
ENSG00000259467	Chromatin interaction
ENSG00000069329	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12438041	0.86[ASN][1000 genomes]
rs12438692	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12438726	0.86[ASN][1000 genomes]
rs12441687	0.88[ASN][1000 genomes]
rs12591072	0.89[ASN][1000 genomes]
rs12591371	0.82[ASN][1000 genomes]
rs12595772	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16963635	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58035812	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61086221	0.90[ASN][1000 genomes]
rs7167333	0.90[ASN][1000 genomes]
rs7174329	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7181866	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8031031	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044277	chr15:49921547-50702386	Enhancers Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542380	chr15:49921547-50702386	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv1045456	chr15:50592472-51019873	Strong transcription Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
4	nsv948579	chr15:50645530-51045564	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 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	chr15:50644000-50646800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr15:50644000-50648600	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr15:50644000-50648600	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr15:50644200-50648200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr15:50644200-50648400	Active TSS	HSMMtube	muscle
6	chr15:50644200-50648600	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr15:50644200-50648800	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr15:50644400-50648200	Active TSS	Primary T killer memory cells from peripheral blood	blood
9	chr15:50644400-50648400	Active TSS	Pancreatic Islets	Pancreatic Islet
10	chr15:50644400-50648800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:50644400-50649000	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr15:50644400-50649200	Active TSS	Fetal Brain Female	brain
13	chr15:50644400-50649400	Active TSS	NHLF	lung
14	chr15:50644600-50647800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:50644600-50648800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:50644600-50649200	Active TSS	H1 Cell Line	embryonic stem cell
17	chr15:50644600-50649200	Active TSS	GM12878-XiMat	blood
18	chr15:50644600-50649800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:50644800-50647800	Active TSS	Colonic Mucosa	Colon
20	chr15:50644800-50648000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:50644800-50648200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:50644800-50648400	Active TSS	Ovary	ovary
23	chr15:50644800-50648600	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr15:50644800-50648600	Active TSS	HMEC	breast
25	chr15:50644800-50648800	Active TSS	Thymus	Thymus
26	chr15:50644800-50649200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr15:50644800-50649200	Active TSS	Right Ventricle	heart
28	chr15:50645000-50646800	Active TSS	Right Atrium	heart
29	chr15:50645000-50647800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
30	chr15:50645000-50647800	Active TSS	Skeletal Muscle Female	skeletal muscle
31	chr15:50645000-50648000	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr15:50645000-50648200	Active TSS	Primary B cells from peripheral blood	blood
33	chr15:50645000-50648200	Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr15:50645000-50648400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr15:50645000-50648400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
36	chr15:50645000-50648400	Active TSS	Aorta	Aorta
37	chr15:50645000-50648400	Active TSS	HSMM	muscle
38	chr15:50645000-50648400	Active TSS	K562	blood
39	chr15:50645000-50648600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:50645000-50648600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr15:50645000-50648600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr15:50645000-50648600	Active TSS	Fetal Intestine Large	intestine
43	chr15:50645000-50648600	Active TSS	Fetal Muscle Trunk	muscle
44	chr15:50645000-50648600	Active TSS	Stomach Smooth Muscle	stomach
45	chr15:50645000-50648800	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr15:50645000-50649000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr15:50645000-50649000	Active TSS	Primary T cells fromperipheralblood	blood
48	chr15:50645000-50649000	Active TSS	Fetal Muscle Leg	muscle
49	chr15:50645000-50649000	Active TSS	NHDF-Ad	bronchial
50	chr15:50645000-50649200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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