Variant report

Variant	rs12911421
Chromosome Location	chr15:75287822-75287823
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	SP4	chr15:75287462-75288014	H1-hESC	embryonic stem cell:	n/a	n/a
2	REST	chr15:75287193-75288199	U87	brain:	n/a	chr15:75287731-75287744 chr15:75287727-75287747 chr15:75287731-75287744 chr15:75287734-75287747 chr15:75288058-75288071 chr15:75287727-75287747 chr15:75287727-75287747 chr15:75287738-75287747 chr15:75287727-75287741 chr15:75287733-75287742
3	FOXA1	chr15:75287612-75287841	T-47D	breast:	n/a	n/a
4	ZNF143	chr15:75287584-75287922	K562	blood:	n/a	n/a
5	RFX5	chr15:75287605-75288013	HepG2	liver:	n/a	n/a
6	STAT3	chr15:75287602-75287865	MCF10A-Er-Src	breast:	n/a	n/a
7	SIN3AK20	chr15:75287571-75287877	PANC-1	pancreas:	n/a	n/a
8	NFYA	chr15:75287724-75287900	Hela-S3	cervix:	n/a	n/a
9	RFX5	chr15:75287560-75287984	Hela-S3	cervix:	n/a	n/a
10	YY1	chr15:75287583-75288035	GM12878	blood:	n/a	chr15:75287849-75287863 chr15:75287908-75287919 chr15:75287849-75287858 chr15:75287904-75287913
11	REST	chr15:75287381-75288635	H1-neurons	neurons:	n/a	chr15:75287731-75287744 chr15:75287727-75287747 chr15:75287731-75287744 chr15:75287734-75287747 chr15:75288058-75288071 chr15:75287727-75287747 chr15:75287727-75287747 chr15:75287738-75287747 chr15:75287727-75287741 chr15:75287733-75287742
12	CBX3	chr15:75287533-75287845	K562	blood:	n/a	n/a
13	SPI1	chr15:75287598-75287877	GM12891	blood:	n/a	n/a
14	HEY1	chr15:75287678-75288119	HepG2	liver:	n/a	chr15:75287850-75287865 chr15:75287710-75287725
15	ZBTB33	chr15:75287620-75288000	HepG2	liver:	n/a	chr15:75287816-75287831 chr15:75287821-75287830 chr15:75287776-75287791
16	HA-E2F1	chr15:75287549-75288173	MCF-7	breast:	n/a	chr15:75287904-75287913 chr15:75287849-75287858
17	SIN3AK20	chr15:75287471-75288050	SK-N-SH	brain:	n/a	n/a
18	REST	chr15:75287598-75287852	PANC-1	pancreas:	n/a	chr15:75287731-75287744 chr15:75287727-75287747 chr15:75287731-75287744 chr15:75287734-75287747 chr15:75287727-75287747 chr15:75287727-75287747 chr15:75287738-75287747 chr15:75287727-75287741 chr15:75287733-75287742
19	RCOR1	chr15:75287548-75287993	GM12878	blood:	n/a	n/a
20	POLR2A	chr15:75287544-75288767	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr15:75287624-75287951	K562	blood:	n/a	n/a
22	SIN3AK20	chr15:75287537-75287872	H1-hESC	embryonic stem cell:	n/a	n/a
23	CHD2	chr15:75287384-75288482	HepG2	liver:	n/a	chr15:75287821-75287830 chr15:75288062-75288072
24	REST	chr15:75287184-75288242	ECC-1	luminal epithelium:	n/a	chr15:75287731-75287744 chr15:75287727-75287747 chr15:75287731-75287744 chr15:75287734-75287747 chr15:75288058-75288071 chr15:75287727-75287747 chr15:75287727-75287747 chr15:75287738-75287747 chr15:75287727-75287741 chr15:75287733-75287742
25	MAX	chr15:75287430-75288048	MCF-7	breast:	n/a	n/a
26	MYC	chr15:75287807-75287929	HepG2	liver:	n/a	n/a
27	REST	chr15:75287308-75287971	HepG2	liver:	n/a	chr15:75287731-75287744 chr15:75287727-75287747 chr15:75287731-75287744 chr15:75287734-75287747 chr15:75287727-75287747 chr15:75287727-75287747 chr15:75287738-75287747 chr15:75287727-75287741 chr15:75287733-75287742
28	MAZ	chr15:75287604-75288064	Hela-S3	cervix:	n/a	n/a
29	MXI1	chr15:75287626-75287957	Hela-S3	cervix:	n/a	n/a
30	MAX	chr15:75287579-75287972	Hela-S3	cervix:	n/a	n/a
31	ZBTB33	chr15:75287475-75288067	K562	blood:	n/a	chr15:75287816-75287831 chr15:75287821-75287830 chr15:75287776-75287791
32	SP4	chr15:75287416-75287924	H1-hESC	embryonic stem cell:	n/a	n/a
33	YY1	chr15:75287535-75288032	K562	blood:	n/a	chr15:75287849-75287863 chr15:75287908-75287919 chr15:75287849-75287858 chr15:75287904-75287913
34	TAF1	chr15:75287357-75288196	H1-neurons	neurons:	n/a	n/a
35	SIN3AK20	chr15:75287574-75287889	K562	blood:	n/a	n/a
36	ZNF143	chr15:75287489-75287928	H1-hESC	embryonic stem cell:	n/a	n/a
37	MAZ	chr15:75287604-75288039	K562	blood:	n/a	n/a
38	MAX	chr15:75287724-75287950	HepG2	liver:	n/a	n/a
39	ETS1	chr15:75287590-75287847	K562	blood:	n/a	chr15:75287813-75287822 chr15:75287821-75287830
40	REST	chr15:75287522-75287954	GM12878	blood:	n/a	chr15:75287731-75287744 chr15:75287727-75287747 chr15:75287731-75287744 chr15:75287734-75287747 chr15:75287727-75287747 chr15:75287727-75287747 chr15:75287738-75287747 chr15:75287727-75287741 chr15:75287733-75287742
41	ELF1	chr15:75287637-75287885	HepG2	liver:	n/a	chr15:75287809-75287822
42	MYC	chr15:75287573-75287924	NB4	blood:	n/a	n/a
43	REST	chr15:75287246-75288065	H1-hESC	embryonic stem cell:	n/a	chr15:75287731-75287744 chr15:75287727-75287747 chr15:75287731-75287744 chr15:75287734-75287747 chr15:75287727-75287747 chr15:75287727-75287747 chr15:75287738-75287747 chr15:75287727-75287741 chr15:75287733-75287742
44	POLR2A	chr15:75287743-75288682	H1-hESC	embryonic stem cell:	n/a	n/a
45	HDAC2	chr15:75287566-75287977	HepG2	liver:	n/a	chr15:75287728-75287747
46	TEAD4	chr15:75287516-75287883	K562	blood:	n/a	n/a
47	PAX5	chr15:75287640-75287842	GM12878	blood:	n/a	n/a
48	MAX	chr15:75287561-75287932	NB4	blood:	n/a	n/a
49	SIN3AK20	chr15:75287558-75287923	A549	lung:	n/a	n/a
50	POLR2A	chr15:75287803-75288017	ProgFib	skin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:75287065..75288881-chr15:75303278..75305678,2	MCF-7	breast:
2	chr15:75287417..75289225-chr15:75314885..75317439,2	MCF-7	breast:
3	chr15:75286200..75292858-chr15:75303462..75309796,11	MCF-7	breast:
4	chr15:75246590..75249281-chr15:75285572..75288569,4	MCF-7	breast:
5	chr15:75286466..75289268-chr15:75313854..75316191,2	MCF-7	breast:
6	chr15:75274950..75276613-chr15:75287594..75290045,3	K562	blood:
7	chr14:81686752..81687294-chr15:75287631..75288229,2	NB4	blood:
8	chr15:75287456..75290010-chr15:75314463..75316098,2	K562	blood:
9	chr15:75275080..75277543-chr15:75287594..75290421,2	K562	blood:

Variant related genes	Relation type
SCAMP5	TF binding region
ENSG00000178718	Chromatin interaction
ENSG00000199580	Chromatin interaction
ENSG00000165417	Chromatin interaction
ENSG00000260483	Chromatin interaction
ENSG00000198794	Chromatin interaction
ENSG00000138621	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1108059	1.00[YRI][hapmap]
rs12050628	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs13056	0.93[TSI][hapmap];0.86[EUR][1000 genomes]
rs1867150	0.85[EUR][1000 genomes]
rs2120019	0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs2120020	0.85[EUR][1000 genomes]
rs2289582	0.85[EUR][1000 genomes]
rs2289583	0.87[CHB][hapmap];0.91[CHD][hapmap];0.86[LWK][hapmap];1.00[YRI][hapmap]
rs2304903	0.95[TSI][hapmap];0.84[EUR][1000 genomes]
rs2415255	0.80[EUR][1000 genomes]
rs34492112	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34713999	0.86[EUR][1000 genomes]
rs34835684	0.80[EUR][1000 genomes]
rs35736167	0.80[EUR][1000 genomes]
rs35911108	0.83[EUR][1000 genomes]
rs3850093	0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs4886414	0.84[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5020842	0.85[EUR][1000 genomes]
rs59094290	0.85[EUR][1000 genomes]
rs60425110	0.80[EUR][1000 genomes]
rs7175720	0.85[TSI][hapmap]
rs8028632	0.95[TSI][hapmap];0.85[EUR][1000 genomes]
rs8030089	0.89[EUR][1000 genomes]
rs8033925	0.86[EUR][1000 genomes]
rs8036573	0.85[EUR][1000 genomes]
rs8042558	0.84[CEU][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap]
rs9672995	0.86[EUR][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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv542435	chr15:75271788-75321117	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12911421	ULK3	cis	parietal	SCAN
rs12911421	GLCE	cis	cerebellum	SCAN
rs12911421	CYP1A1	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75286600-75288400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
2	chr15:75286600-75289000	Active TSS	Brain Substantia Nigra	brain
3	chr15:75286600-75289600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr15:75286800-75288600	Active TSS	Brain Cingulate Gyrus	brain
5	chr15:75286800-75288800	Active TSS	Brain Angular Gyrus	brain
6	chr15:75287000-75288600	Active TSS	Brain Hippocampus Middle	brain
7	chr15:75287200-75288000	Active TSS	Sigmoid Colon	Sigmoid Colon
8	chr15:75287200-75288000	Active TSS	Stomach Smooth Muscle	stomach
9	chr15:75287200-75288200	Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr15:75287200-75288600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr15:75287200-75289800	Active TSS	H9 Cell Line	embryonic stem cell
12	chr15:75287400-75288000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
13	chr15:75287400-75288000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr15:75287400-75288000	Enhancers	Placenta	Placenta
15	chr15:75287400-75288000	Enhancers	Gastric	stomach
16	chr15:75287400-75288000	Active TSS	Lung	lung
17	chr15:75287400-75288000	Active TSS	Small Intestine	intestine
18	chr15:75287400-75288000	Active TSS	HMEC	breast
19	chr15:75287400-75288000	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
20	chr15:75287400-75288200	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr15:75287400-75288200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:75287400-75288200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr15:75287400-75288200	Active TSS	Duodenum Mucosa	Duodenum
24	chr15:75287400-75288200	Active TSS	Psoas Muscle	Psoas
25	chr15:75287400-75288200	Active TSS	NHEK	skin
26	chr15:75287400-75288400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr15:75287400-75288400	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr15:75287400-75288400	Active TSS	Colonic Mucosa	Colon
29	chr15:75287400-75288400	Active TSS	Left Ventricle	heart
30	chr15:75287400-75288400	Active TSS	Rectal Smooth Muscle	rectum
31	chr15:75287400-75288400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr15:75287400-75288600	Active TSS	HUES48 Cell Line	embryonic stem cell
33	chr15:75287400-75288600	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr15:75287400-75288600	Active TSS	iPS-20b Cell Line	embryonic stem cell
35	chr15:75287400-75288600	Active TSS	Primary T cells from cord blood	blood
36	chr15:75287400-75288600	Active TSS	Brain Inferior Temporal Lobe	brain
37	chr15:75287400-75288600	Active TSS	GM12878-XiMat	blood
38	chr15:75287400-75288600	Active TSS	HSMM	muscle
39	chr15:75287400-75288800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:75287400-75288800	Bivalent/Poised TSS	Muscle Satellite Cultured Cells	--
41	chr15:75287400-75288800	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr15:75287400-75288800	Enhancers	Fetal Lung	lung
43	chr15:75287400-75288800	Flanking Active TSS	Dnd41	blood
44	chr15:75287400-75290000	Bivalent Enhancer	Stomach Mucosa	stomach
45	chr15:75287600-75288000	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr15:75287600-75288000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:75287600-75288000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:75287600-75288000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
49	chr15:75287600-75288000	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
50	chr15:75287600-75288000	Active TSS	Primary hematopoietic stem cells short term culture	blood

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