Variant report

Variant	rs17551416
Chromosome Location	chr15:44828723-44828724
allele	C/G
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	chr15:44828559-44829562	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:44828630-44829790	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZBTB7A	chr15:44828454-44829193	ECC-1	luminal epithelium:	n/a	n/a
4	TAF1	chr15:44828583-44829532	PFSK-1	brain:	n/a	n/a
5	CEBPB	chr15:44828125-44829549	Hela-S3	cervix:	n/a	n/a
6	PAX5	chr15:44828570-44829077	GM12892	blood:	n/a	n/a
7	POLR2A	chr15:44828642-44829118	A549	lung:	n/a	n/a
8	POLR2A	chr15:44828477-44829128	U87	brain:	n/a	n/a
9	POLR2A	chr15:44828228-44830231	GM19193	blood:	n/a	n/a
10	MAX	chr15:44828246-44830328	NB4	blood:	n/a	chr15:44829900-44829909 chr15:44829901-44829911 chr15:44829903-44829910
11	MAX	chr15:44828346-44830188	SK-N-SH	brain:	n/a	chr15:44829900-44829909 chr15:44829901-44829911 chr15:44829903-44829910
12	HEY1	chr15:44828119-44830513	K562	blood:	n/a	chr15:44829649-44829664 chr15:44829633-44829648
13	E2F6	chr15:44828601-44829021	A549	lung:	n/a	n/a
14	YY1	chr15:44828381-44829115	GM12878	blood:	n/a	n/a
15	BCLAF1	chr15:44828364-44829106	GM12878	blood:	n/a	n/a
16	UBTF	chr15:44828644-44828970	K562	blood:	n/a	n/a
17	MAX	chr15:44828282-44830278	HCT-116	colon:	n/a	chr15:44829900-44829909 chr15:44829901-44829911 chr15:44829903-44829910
18	POLR2A	chr15:44828662-44829118	SK-N-SH	brain:	n/a	n/a
19	POLR2A	chr15:44827952-44830503	K562	blood:	n/a	n/a
20	E2F6	chr15:44828432-44830192	A549	lung:	n/a	chr15:44829201-44829213 chr15:44829232-44829242 chr15:44829705-44829715
21	POLR2A	chr15:44828206-44830355	HepG2	liver:	n/a	n/a
22	RCOR1	chr15:44828640-44828982	K562	blood:	n/a	n/a
23	CTCF	chr15:44828709-44829082	IMR90	lung:	n/a	n/a
24	TBP	chr15:44828603-44830374	K562	blood:	n/a	n/a
25	TBP	chr15:44828690-44829508	HepG2	liver:	n/a	n/a
26	TAF1	chr15:44828658-44829120	GM12878	blood:	n/a	n/a
27	REST	chr15:44828510-44829111	SK-N-SH	brain:	n/a	n/a
28	FOS	chr15:44828611-44829955	HUVEC	blood vessel:	n/a	chr15:44829322-44829333 chr15:44829324-44829333
29	STAT3	chr15:44828499-44829040	MCF10A-Er-Src	breast:	n/a	n/a
30	HEY1	chr15:44828580-44829116	HepG2	liver:	n/a	n/a
31	MYC	chr15:44828485-44830455	MCF10A-Er-Src	breast:	n/a	chr15:44829900-44829909 chr15:44829901-44829911 chr15:44829903-44829910
32	HEY1	chr15:44828145-44829653	HepG2	liver:	n/a	chr15:44829633-44829648
33	EP300	chr15:44828441-44829362	HepG2	liver:	n/a	chr15:44829232-44829241
34	YY1	chr15:44828642-44829074	HCT-116	colon:	n/a	n/a
35	MAZ	chr15:44828193-44830453	IMR90	lung:	n/a	chr15:44829900-44829909 chr15:44829901-44829911 chr15:44829903-44829910
36	POLR2A	chr15:44828237-44829669	U87	brain:	n/a	n/a
37	CREB1	chr15:44828566-44829978	HepG2	liver:	n/a	n/a
38	TAF1	chr15:44828463-44829637	SK-N-SH	brain:	n/a	n/a
39	TAF1	chr15:44828710-44829106	Hela-S3	cervix:	n/a	n/a
40	MAX	chr15:44828426-44829374	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr15:44828281-44829870	K562	blood:	n/a	n/a
42	POLR2A	chr15:44828550-44830045	GM12878	blood:	n/a	n/a
43	TCF7L2	chr15:44828682-44829675	HCT-116	colon:	n/a	chr15:44829323-44829332 chr15:44829324-44829333
44	POLR2A	chr15:44828486-44829721	ECC-1	luminal epithelium:	n/a	n/a
45	MYC	chr15:44828714-44828727	HUVEC	blood vessel:	n/a	n/a
46	CEBPD	chr15:44828583-44829639	HepG2	liver:	n/a	n/a
47	POLR2A	chr15:44828474-44830283	K562	blood:	n/a	n/a
48	POLR2A	chr15:44828245-44829973	Raji	blood:	n/a	n/a
49	POLR2A	chr15:44828263-44830089	HUVEC	blood vessel:	n/a	n/a
50	MAX	chr15:44828215-44830311	A549	lung:	n/a	chr15:44829900-44829909 chr15:44829901-44829911 chr15:44829903-44829910

No.	Distal block	Cell Line	Cell type
1	chr15:44562480..44565823-chr15:44827596..44830231,3	K562	blood:
2	chr15:44828247..44829224-chr2:88927152..88927802,2	Hela-S3	cervix:
3	chr15:44589545..44591390-chr15:44828180..44830193,2	K562	blood:
4	chr15:44580146..44582349-chr15:44827451..44829460,2	MCF-7	breast:
5	chr15:44828640..44829478-chr15:59225791..59226422,2	Hela-S3	cervix:
6	chr15:44828452..44828958-chr2:85765826..85766351,2	Hela-S3	cervix:
7	chr1:33282965..33283792-chr15:44828603..44829430,2	Hela-S3	cervix:
8	chr1:11968060..11968659-chr15:44827984..44829180,3	Hela-S3	cervix:
9	chr15:44828615..44829474-chr16:74734365..74734926,2	Hela-S3	cervix:
10	chr15:44828679..44830776-chr15:44954210..44955982,2	K562	blood:
11	chr15:44828586..44829376-chrX:47420268..47421097,2	Hela-S3	cervix:
12	chr15:44562480..44564339-chr15:44827596..44829843,2	K562	blood:
13	chr10:74856476..74857087-chr15:44828192..44829008,2	NB4	blood:
14	chr15:44828386..44829084-chr3:25705757..25706421,2	Hela-S3	cervix:
15	chr15:44827999..44828935-chr6:109703239..109703989,2	Hela-S3	cervix:
16	chr1:108742388..108743214-chr15:44828445..44829131,2	Hela-S3	cervix:
17	chr15:44828266..44829096-chr16:67597371..67597967,2	Hela-S3	cervix:
18	chr15:44828332..44829115-chr9:86594438..86595354,2	Hela-S3	cervix:
19	chr15:44828596..44829329-chr22:50354040..50354887,2	HCT-116	colon:
20	chr1:173836321..173837263-chr15:44828452..44829299,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SPG11-1	chr15:44828241-44828838	ENSG00000179523.4
2	lnc-SPG11-1	chr15:44828241-44829121	ENSG00000179523.4
3	lnc-SPG11-1	chr15:44828364-44828743	NONHSAT042166
4	lnc-SPG11-1	chr15:44828241-44829121	NR_034170

Variant related genes	Relation type
EIF3J	TF binding region
EIF3J-AS1	TF binding region
ENSG00000260879	Chromatin interaction
ENSG00000168404	Chromatin interaction
ENSG00000234028	Chromatin interaction
ENSG00000168906	Chromatin interaction
ENSG00000203575	Chromatin interaction
ENSG00000166734	Chromatin interaction
ENSG00000078061	Chromatin interaction
ENSG00000185278	Chromatin interaction
ENSG00000203578	Chromatin interaction
ENSG00000137776	Chromatin interaction
ENSG00000104133	Chromatin interaction
ENSG00000077097	Chromatin interaction
ENSG00000198355	Chromatin interaction
ENSG00000134684	Chromatin interaction
ENSG00000165119	Chromatin interaction
ENSG00000135535	Chromatin interaction
ENSG00000199347	Chromatin interaction
ENSG00000122884	Chromatin interaction
ENSG00000116497	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000261386	Chromatin interaction
ENSG00000085491	Chromatin interaction

Extended variants
information (count: 89 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10152710	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1021800	1.00[EUR][1000 genomes]
rs10467977	0.94[EUR][1000 genomes]
rs12591178	0.94[EUR][1000 genomes]
rs12591581	1.00[EUR][1000 genomes]
rs12591811	0.88[EUR][1000 genomes]
rs12592995	0.94[EUR][1000 genomes]
rs12593125	0.94[EUR][1000 genomes]
rs12593325	1.00[EUR][1000 genomes]
rs12593686	0.88[EUR][1000 genomes]
rs12593943	0.88[EUR][1000 genomes]
rs12594110	1.00[EUR][1000 genomes]
rs12594139	0.88[EUR][1000 genomes]
rs12594167	0.94[EUR][1000 genomes]
rs12594621	0.88[EUR][1000 genomes]
rs12594645	0.88[EUR][1000 genomes]
rs12594746	0.94[EUR][1000 genomes]
rs12595484	0.88[EUR][1000 genomes]
rs2055061	0.94[EUR][1000 genomes]
rs2277610	0.83[ASN][1000 genomes]
rs2288341	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2288342	0.94[EUR][1000 genomes]
rs2303577	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2303578	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2412883	0.94[EUR][1000 genomes]
rs2412909	0.94[EUR][1000 genomes]
rs2433350	0.94[EUR][1000 genomes]
rs2555353	0.94[EUR][1000 genomes]
rs2556566	0.94[EUR][1000 genomes]
rs2556567	0.88[EUR][1000 genomes]
rs28508235	0.88[EUR][1000 genomes]
rs28561508	0.94[EUR][1000 genomes]
rs2899113	1.00[EUR][1000 genomes]
rs35555389	0.94[EUR][1000 genomes]
rs3784565	0.94[EUR][1000 genomes]
rs3784567	0.94[EUR][1000 genomes]
rs3809471	0.94[EUR][1000 genomes]
rs3816928	0.94[EUR][1000 genomes]
rs3986142	0.94[EUR][1000 genomes]
rs3986143	0.94[EUR][1000 genomes]
rs4415978	0.94[EUR][1000 genomes]
rs4477677	0.94[EUR][1000 genomes]
rs4577056	0.94[EUR][1000 genomes]
rs57270586	0.94[EUR][1000 genomes]
rs58956090	0.94[EUR][1000 genomes]
rs59230801	0.94[EUR][1000 genomes]
rs59997416	0.88[EUR][1000 genomes]
rs60003667	0.94[EUR][1000 genomes]
rs60399672	0.94[EUR][1000 genomes]
rs61185650	0.94[EUR][1000 genomes]
rs61234123	0.94[EUR][1000 genomes]
rs61258861	0.94[EUR][1000 genomes]
rs61278540	0.88[EUR][1000 genomes]
rs61329003	0.94[EUR][1000 genomes]
rs61501839	0.94[EUR][1000 genomes]
rs6493103	0.88[EUR][1000 genomes]
rs7162671	0.88[EUR][1000 genomes]
rs7162802	0.88[EUR][1000 genomes]
rs7163529	0.88[EUR][1000 genomes]
rs7164709	0.88[EUR][1000 genomes]
rs7166278	0.94[EUR][1000 genomes]
rs7166945	0.94[EUR][1000 genomes]
rs7167752	0.88[EUR][1000 genomes]
rs7169333	0.94[EUR][1000 genomes]
rs7170248	0.94[EUR][1000 genomes]
rs7172106	0.94[EUR][1000 genomes]
rs7175200	0.88[EUR][1000 genomes]
rs7178318	0.94[EUR][1000 genomes]
rs7179894	0.88[EUR][1000 genomes]
rs7181772	0.94[EUR][1000 genomes]
rs7183109	0.83[EUR][1000 genomes]
rs8023453	0.94[EUR][1000 genomes]
rs8024623	0.88[EUR][1000 genomes]
rs8024805	0.88[EUR][1000 genomes]
rs8025727	0.88[EUR][1000 genomes]
rs8025876	0.94[EUR][1000 genomes]
rs8025955	0.88[EUR][1000 genomes]
rs8026945	0.94[EUR][1000 genomes]
rs8027036	0.94[EUR][1000 genomes]
rs8028509	0.94[EUR][1000 genomes]
rs8028907	0.88[EUR][1000 genomes]
rs8032079	0.88[EUR][1000 genomes]
rs8037395	0.88[EUR][1000 genomes]
rs883943	0.94[EUR][1000 genomes]
rs9672237	0.94[EUR][1000 genomes]
rs9673085	0.94[EUR][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	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
2	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak 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	154 gene(s)	inside rSNPs	diseases
3	esv3386433	chr15:44654644-45037538	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription 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 miRNA target site	135 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	chr15:44827600-44830200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr15:44827600-44830400	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr15:44827600-44830600	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr15:44827600-44830600	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr15:44827600-44831000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:44827800-44828800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr15:44827800-44829800	Active TSS	Brain Cingulate Gyrus	brain
8	chr15:44827800-44830000	Active TSS	Brain Anterior Caudate	brain
9	chr15:44827800-44830200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr15:44827800-44830200	Active TSS	iPS-15b Cell Line	embryonic stem cell
11	chr15:44827800-44830200	Active TSS	Fetal Intestine Small	intestine
12	chr15:44827800-44830400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr15:44827800-44830600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr15:44827800-44830600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr15:44827800-44830800	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr15:44827800-44830800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr15:44827800-44830800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:44827800-44830800	Active TSS	HSMM	muscle
19	chr15:44827800-44830800	Active TSS	NHDF-Ad	bronchial
20	chr15:44827800-44831000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr15:44828000-44828800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
22	chr15:44828000-44828800	Flanking Active TSS	Primary B cells from cord blood	blood
23	chr15:44828000-44828800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
24	chr15:44828000-44828800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:44828000-44828800	Flanking Active TSS	Fetal Muscle Leg	muscle
26	chr15:44828000-44828800	Flanking Active TSS	Dnd41	blood
27	chr15:44828000-44829000	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr15:44828000-44829600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr15:44828000-44830000	Active TSS	Brain Angular Gyrus	brain
30	chr15:44828000-44830200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr15:44828000-44830200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:44828000-44830200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:44828000-44830200	Active TSS	Colon Smooth Muscle	Colon
34	chr15:44828000-44830200	Active TSS	Fetal Intestine Large	intestine
35	chr15:44828000-44830200	Active TSS	Fetal Kidney	kidney
36	chr15:44828000-44830400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr15:44828000-44830400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:44828000-44830400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr15:44828000-44830400	Active TSS	Esophagus	oesophagus
40	chr15:44828000-44830400	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr15:44828000-44830400	Active TSS	Gastric	stomach
42	chr15:44828000-44830400	Active TSS	Ovary	ovary
43	chr15:44828000-44830400	Active TSS	Stomach Mucosa	stomach
44	chr15:44828000-44830600	Active TSS	H1 Cell Line	embryonic stem cell
45	chr15:44828000-44830600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:44828000-44830600	Active TSS	Right Atrium	heart
47	chr15:44828000-44830600	Active TSS	A549	lung
48	chr15:44828000-44831000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr15:44828000-44831000	Active TSS	Psoas Muscle	Psoas
50	chr15:44828000-44831200	Active TSS	HSMMtube	muscle

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