Variant report

Variant	rs4653666
Chromosome Location	chr1:225945051-225945052
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:225942220..225946918-chr1:225947468..225951068,4	K562	blood:

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10915873	0.80[EUR][1000 genomes]
rs12141610	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1557092	0.95[CEU][hapmap];0.85[CHB][hapmap];0.91[CHD][hapmap];0.92[GIH][hapmap]
rs2126345	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2487691	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2615067	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2615076	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4653669	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4653670	0.84[CHB][hapmap];0.82[EUR][1000 genomes]
rs4653674	0.91[CEU][hapmap]
rs6659660	0.91[CEU][hapmap]
rs7532460	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7535106	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs898848	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv832736	chr1:225815717-225968619	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4653666	PSEN2	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225935000-225949600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:225938600-225945200	Weak transcription	Small Intestine	intestine
3	chr1:225939200-225949600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr1:225939800-225945800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:225943200-225946600	Enhancers	Fetal Muscle Trunk	muscle
6	chr1:225943400-225945600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr1:225943400-225949400	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:225943400-225949800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr1:225943400-225951800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:225943600-225945200	Weak transcription	Fetal Intestine Small	intestine
11	chr1:225943600-225945600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr1:225943600-225949800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:225943600-225951400	Weak transcription	Pancreas	Pancrea
14	chr1:225943600-225951800	Weak transcription	Gastric	stomach
15	chr1:225943600-225954800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:225943800-225945200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:225943800-225945800	Weak transcription	Esophagus	oesophagus
18	chr1:225943800-225948400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:225943800-225949800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr1:225943800-225951200	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:225944000-225945200	Weak transcription	Fetal Intestine Large	intestine
22	chr1:225944000-225945800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:225944000-225945800	Weak transcription	Fetal Lung	lung
24	chr1:225944000-225945800	Weak transcription	Fetal Thymus	thymus
25	chr1:225944000-225945800	Weak transcription	HSMMtube	muscle
26	chr1:225944000-225949400	Weak transcription	A549	lung
27	chr1:225944000-225949600	Weak transcription	Right Atrium	heart
28	chr1:225944200-225945400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr1:225944200-225945800	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:225944200-225945800	Weak transcription	Ovary	ovary
31	chr1:225944200-225945800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr1:225944200-225946000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:225944200-225949200	Weak transcription	NH-A	brain
34	chr1:225944200-225949400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:225944200-225949400	Weak transcription	NHLF	lung
36	chr1:225944200-225949600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr1:225944200-225949600	Weak transcription	HSMM	muscle
38	chr1:225944200-225951800	Weak transcription	Right Ventricle	heart
39	chr1:225944400-225945800	Weak transcription	Lung	lung
40	chr1:225944400-225945800	Weak transcription	Spleen	Spleen
41	chr1:225944400-225945800	Weak transcription	NHDF-Ad	bronchial
42	chr1:225944400-225946000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:225944400-225948200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:225944400-225949200	Weak transcription	Osteobl	bone
45	chr1:225944400-225949400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr1:225944400-225949600	Weak transcription	Left Ventricle	heart
47	chr1:225944800-225948600	Weak transcription	HepG2	liver
48	chr1:225945000-225946000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr1:225945000-225946200	Enhancers	Duodenum Mucosa	Duodenum

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