Variant report

Variant	rs12758915
Chromosome Location	chr1:227058344-227058345
allele	A/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	MTA3	chr1:227057944-227058344	GM12878	blood:	n/a	n/a
2	ETS1	chr1:227057978-227058935	K562	blood:	n/a	chr1:227058761-227058772 chr1:227057995-227058004 chr1:227058535-227058546 chr1:227058353-227058364
3	SMC3	chr1:227058149-227058818	K562	blood:	n/a	chr1:227058203-227058213 chr1:227058493-227058503 chr1:227058562-227058572
4	CTCF	chr1:227057993-227058404	H1-hESC	embryonic stem cell:	n/a	chr1:227057994-227058007
5	MAX	chr1:227057691-227059199	A549	lung:	n/a	chr1:227058761-227058771
6	UBTF	chr1:227057938-227058925	K562	blood:	n/a	n/a
7	ESR1	chr1:227058049-227058510	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr1:227057976-227058759	ProgFib	skin:	n/a	n/a
9	POLR2A	chr1:227057955-227058793	K562	blood:	n/a	n/a
10	POLR2A	chr1:227058273-227058406	H1-hESC	embryonic stem cell:	n/a	n/a
11	HCFC1	chr1:227057704-227059057	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr1:227058232-227058790	HepG2	liver:	n/a	n/a
13	ZBTB7A	chr1:227057896-227059105	ECC-1	luminal epithelium:	n/a	n/a
14	ZBTB7A	chr1:227058007-227058987	K562	blood:	n/a	n/a
15	JUND	chr1:227057814-227058624	K562	blood:	n/a	n/a
16	CEBPB	chr1:227057947-227058601	Hela-S3	cervix:	n/a	n/a
17	EP300	chr1:227058094-227058601	T-47D	breast:	n/a	chr1:227058560-227058576
18	CREB1	chr1:227057896-227058709	A549	lung:	n/a	n/a
19	MYC	chr1:227058081-227058630	MCF-7	breast:	n/a	n/a
20	POLR2A	chr1:227057936-227058769	HepG2	liver:	n/a	n/a
21	ZBTB7A	chr1:227058121-227058953	ECC-1	luminal epithelium:	n/a	n/a
22	MAFK	chr1:227058128-227058706	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr1:227057917-227058737	Hela-S3	cervix:	n/a	n/a
24	HDAC2	chr1:227057881-227058720	MCF-7	breast:	n/a	n/a
25	POLR2A	chr1:227057971-227058676	NB4	blood:	n/a	n/a
26	IRF1	chr1:227058128-227058932	K562	blood:	n/a	chr1:227058536-227058550 chr1:227058645-227058654
27	RAD21	chr1:227058139-227058623	H1-hESC	embryonic stem cell:	n/a	chr1:227058516-227058529 chr1:227058442-227058454
28	EGR1	chr1:227058282-227058861	GM12878	blood:	n/a	chr1:227058532-227058546 chr1:227058686-227058696 chr1:227058533-227058547 chr1:227058532-227058545 chr1:227058534-227058544 chr1:227058532-227058545 chr1:227058535-227058544 chr1:227058761-227058774 chr1:227058760-227058775 chr1:227058687-227058697 chr1:227058532-227058545 chr1:227058531-227058546 chr1:227058761-227058774 chr1:227058528-227058550 chr1:227058535-227058545 chr1:227058501-227058510 chr1:227058761-227058774 chr1:227058761-227058775 chr1:227058762-227058773 chr1:227058682-227058695 chr1:227058764-227058773 chr1:227058760-227058770 chr1:227058757-227058779 chr1:227058532-227058545
29	POLR2A	chr1:227058223-227058499	H1-hESC	embryonic stem cell:	n/a	n/a
30	USF1	chr1:227058263-227058962	ECC-1	luminal epithelium:	n/a	chr1:227058884-227058897 chr1:227058689-227058705 chr1:227058385-227058401 chr1:227058559-227058575
31	MAX	chr1:227057775-227059120	HCT-116	colon:	n/a	chr1:227058761-227058771
32	SMC3	chr1:227057880-227059275	Hela-S3	cervix:	n/a	chr1:227058203-227058213 chr1:227057902-227057909 chr1:227058493-227058503 chr1:227058562-227058572
33	BHLHE40	chr1:227057895-227059083	GM12878	blood:	n/a	chr1:227058884-227058897 chr1:227058689-227058705 chr1:227058385-227058401 chr1:227058559-227058575
34	BRCA1	chr1:227057790-227058505	Hela-S3	cervix:	n/a	n/a
35	TCF7L2	chr1:227057856-227058759	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:227058087-227058729	MCF-7	breast:	n/a	n/a
37	POLR2A	chr1:227057918-227058777	K562	blood:	n/a	n/a
38	POLR2A	chr1:227057920-227058853	K562	blood:	n/a	n/a
39	EGR1	chr1:227058292-227058881	GM12878	blood:	n/a	chr1:227058532-227058546 chr1:227058686-227058696 chr1:227058533-227058547 chr1:227058532-227058545 chr1:227058534-227058544 chr1:227058532-227058545 chr1:227058535-227058544 chr1:227058761-227058774 chr1:227058760-227058775 chr1:227058687-227058697 chr1:227058532-227058545 chr1:227058531-227058546 chr1:227058761-227058774 chr1:227058528-227058550 chr1:227058535-227058545 chr1:227058501-227058510 chr1:227058761-227058774 chr1:227058761-227058775 chr1:227058762-227058773 chr1:227058682-227058695 chr1:227058764-227058773 chr1:227058760-227058770 chr1:227058757-227058779 chr1:227058532-227058545
40	CTCF	chr1:227058305-227058824	K562	blood:	n/a	chr1:227058559-227058572
41	POLR2A	chr1:227058074-227058717	HCT-116	colon:	n/a	n/a
42	E2F6	chr1:227057968-227058934	K562	blood:	n/a	chr1:227058566-227058576
43	POLR2A	chr1:227058233-227058482	HepG2	liver:	n/a	n/a
44	E2F6	chr1:227057870-227059038	K562	blood:	n/a	chr1:227058566-227058576
45	POLR2A	chr1:227057955-227058765	HCT-116	colon:	n/a	n/a
46	EP300	chr1:227058033-227058548	K562	blood:	n/a	n/a
47	USF2	chr1:227058305-227058889	GM12878	blood:	n/a	chr1:227058689-227058705 chr1:227058385-227058401 chr1:227058559-227058575
48	YY1	chr1:227058076-227058616	HCT-116	colon:	n/a	chr1:227058421-227058435 chr1:227058559-227058573
49	SIN3AK20	chr1:227057917-227059031	K562	blood:	n/a	n/a
50	RCOR1	chr1:227057939-227058790	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:227058010..227060717-chr1:227127922..227130467,2	K562	blood:

Variant related genes	Relation type
PSEN2	TF binding region
ENSG00000163050	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1046240	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1150897	0.88[EUR][1000 genomes]
rs1150900	0.88[EUR][1000 genomes]
rs12086302	0.86[EUR][1000 genomes]
rs1295638	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1295641	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1295643	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1295647	0.81[EUR][1000 genomes]
rs1296171	0.89[EUR][1000 genomes]
rs1794038	0.81[EUR][1000 genomes]
rs2236914	0.87[EUR][1000 genomes]
rs2236915	0.87[EUR][1000 genomes]
rs2793461	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2855559	0.87[EUR][1000 genomes]
rs2855560	0.87[EUR][1000 genomes]
rs2855564	0.86[EUR][1000 genomes]
rs4653470	0.87[EUR][1000 genomes]
rs6759	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7530245	0.83[EUR][1000 genomes]
rs7530370	0.85[EUR][1000 genomes]
rs8383	0.87[EUR][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	nsv4766	chr1:227025954-227070961	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3381082	chr1:227029266-227059927	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12758915	PSEN2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227057600-227058600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr1:227057600-227058600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:227057600-227059000	Active TSS	H9 Cell Line	embryonic stem cell
4	chr1:227057600-227059000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:227057600-227059200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr1:227057800-227058600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:227057800-227058600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:227057800-227058600	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
9	chr1:227057800-227058800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr1:227057800-227058800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:227057800-227058800	Active TSS	Cortex derived primary cultured neurospheres	brain
12	chr1:227057800-227058800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:227057800-227058800	Active TSS	Brain Cingulate Gyrus	brain
14	chr1:227057800-227058800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
15	chr1:227057800-227058800	Bivalent/Poised TSS	Fetal Stomach	stomach
16	chr1:227057800-227058800	Active TSS	Rectal Mucosa Donor 29	rectum
17	chr1:227057800-227058800	Active TSS	Right Ventricle	heart
18	chr1:227057800-227058800	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr1:227057800-227058800	Active TSS	HSMM	muscle
20	chr1:227057800-227059000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr1:227057800-227059000	Active TSS	iPS-15b Cell Line	embryonic stem cell
22	chr1:227057800-227059000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr1:227057800-227059000	Active TSS	Aorta	Aorta
24	chr1:227057800-227059000	Active TSS	Brain Angular Gyrus	brain
25	chr1:227057800-227059000	Active TSS	Brain Hippocampus Middle	brain
26	chr1:227057800-227059000	Active TSS	Brain Inferior Temporal Lobe	brain
27	chr1:227057800-227059000	Active TSS	Fetal Kidney	kidney
28	chr1:227057800-227059000	Active TSS	Psoas Muscle	Psoas
29	chr1:227057800-227059000	Active TSS	Rectal Smooth Muscle	rectum
30	chr1:227057800-227059000	Active TSS	HSMMtube	muscle
31	chr1:227057800-227059200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:227057800-227059200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:227057800-227059200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr1:227057800-227059200	Bivalent/Poised TSS	Primary T cells from cord blood	blood
35	chr1:227057800-227059200	Active TSS	Fetal Brain Female	brain
36	chr1:227057800-227059200	Active TSS	Left Ventricle	heart
37	chr1:227057800-227059200	Active TSS	Right Atrium	heart
38	chr1:227057800-227059600	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr1:227057800-227059800	Flanking Active TSS	Stomach Smooth Muscle	stomach
40	chr1:227057800-227060600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:227058000-227058400	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
42	chr1:227058000-227058400	Bivalent/Poised TSS	Thymus	Thymus
43	chr1:227058000-227058600	Active TSS	HUES48 Cell Line	embryonic stem cell
44	chr1:227058000-227058600	Bivalent/Poised TSS	Primary T helper cells PMA-I stimulated	--
45	chr1:227058000-227058600	Bivalent/Poised TSS	Primary T regulatory cells fromperipheralblood	blood
46	chr1:227058000-227058600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:227058000-227058600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr1:227058000-227058600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr1:227058000-227058600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
50	chr1:227058000-227058600	Active TSS	Fetal Lung	lung

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