Variant report

Variant	rs1877724
Chromosome Location	chr1:226013355-226013356
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	POLR2A	chr1:226011974-226013818	A549	lung:	n/a	n/a
2	MAX	chr1:226012642-226013579	HepG2	liver:	n/a	n/a
3	POLR2A	chr1:226012764-226013364	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
EPHX1	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12031296	1.00[JPT][hapmap]
rs12042925	1.00[JPT][hapmap]
rs1883013	0.87[ASN][1000 genomes]
rs2671270	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2854447	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2854448	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2854451	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2854456	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3820231	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1795046	chr1:225874059-226091150	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv1834932	chr1:225874059-226091150	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv947519	chr1:225998770-226034631	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1877724	PSEN2	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226000000-226019400	Weak transcription	Fetal Brain Female	brain
2	chr1:226000400-226015800	Enhancers	Ovary	ovary
3	chr1:226001800-226019200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:226005600-226019400	Weak transcription	Brain Germinal Matrix	brain
5	chr1:226005800-226013400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:226005800-226019200	Weak transcription	NHLF	lung
7	chr1:226005800-226019400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr1:226005800-226019400	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr1:226006200-226013600	Weak transcription	Small Intestine	intestine
10	chr1:226006200-226016600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:226006200-226019400	Weak transcription	HSMM	muscle
12	chr1:226006200-226022000	Weak transcription	NHDF-Ad	bronchial
13	chr1:226006400-226014200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr1:226006400-226014800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr1:226006400-226016800	Weak transcription	Colonic Mucosa	Colon
16	chr1:226006400-226018600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr1:226006400-226019400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:226006400-226019600	Weak transcription	Hela-S3	cervix
19	chr1:226006600-226016600	Weak transcription	Aorta	Aorta
20	chr1:226008800-226013400	Weak transcription	HMEC	breast
21	chr1:226008800-226019400	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:226009400-226013400	Genic enhancers	Fetal Lung	lung
23	chr1:226009800-226015400	Enhancers	Colon Smooth Muscle	Colon
24	chr1:226010200-226013600	Enhancers	Brain Substantia Nigra	brain
25	chr1:226010400-226015000	Enhancers	Gastric	stomach
26	chr1:226010800-226015400	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr1:226010800-226016600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr1:226010800-226019200	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr1:226011000-226013600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr1:226011000-226013800	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr1:226011000-226014600	Enhancers	Right Atrium	heart
32	chr1:226011000-226015200	Enhancers	Brain Hippocampus Middle	brain
33	chr1:226011000-226015800	Enhancers	Fetal Muscle Trunk	muscle
34	chr1:226011000-226015800	Genic enhancers	Fetal Muscle Leg	muscle
35	chr1:226011000-226016800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr1:226011200-226013600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr1:226011200-226013800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:226011200-226014000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:226011200-226014400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:226011200-226015000	Enhancers	Right Ventricle	heart
41	chr1:226011200-226015600	Enhancers	K562	blood
42	chr1:226011200-226016600	Enhancers	Pancreas	Pancrea
43	chr1:226011400-226013600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
44	chr1:226011600-226013600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:226011600-226013800	Enhancers	H1 Cell Line	embryonic stem cell
46	chr1:226011600-226014000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr1:226011600-226015000	Enhancers	Stomach Mucosa	stomach
48	chr1:226011600-226015200	Genic enhancers	Fetal Intestine Small	intestine
49	chr1:226011800-226013400	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr1:226011800-226013400	Enhancers	Adipose Nuclei	Adipose

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