Variant report

Variant	rs4653669
Chromosome Location	chr1:225950545-225950546
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:225948785..225952549-chr1:225953599..225956527,4	MCF-7	breast:
2	chr1:225942220..225946918-chr1:225947468..225951068,4	K562	blood:
3	chr1:225948184..225950809-chr1:225971310..225972848,2	K562	blood:
4	chr1:225945507..225952186-chr1:225952608..225958481,10	MCF-7	breast:
5	chr1:225890091..225891751-chr1:225949854..225952122,2	MCF-7	breast:
6	chr1:225948046..225950619-chr1:225959798..225962169,2	MCF-7	breast:

Extended variants
information (count: 17 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12141610	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1557092	0.85[CHB][hapmap];0.91[CHD][hapmap];0.81[JPT][hapmap]
rs1809310	0.98[AFR][1000 genomes]
rs2126345	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2487691	0.96[ASN][1000 genomes]
rs2615067	0.80[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2615076	0.84[ASN][1000 genomes]
rs4653666	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4653670	0.84[CHB][hapmap]
rs6685014	0.92[CEU][hapmap];0.91[TSI][hapmap];0.91[EUR][1000 genomes]
rs7532460	0.98[ASN][1000 genomes]
rs7535106	0.84[ASN][1000 genomes]
rs898848	0.83[AMR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4653669	TLR5	cis	cerebellum	SCAN
rs4653669	PSEN2	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:225943400-225951800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:225943600-225951400	Weak transcription	Pancreas	Pancrea
3	chr1:225943600-225951800	Weak transcription	Gastric	stomach
4	chr1:225943600-225954800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr1:225943800-225951200	Weak transcription	Brain Hippocampus Middle	brain
6	chr1:225944200-225951800	Weak transcription	Right Ventricle	heart
7	chr1:225946200-225959800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr1:225946600-225951200	Weak transcription	Lung	lung
9	chr1:225946600-225951200	Weak transcription	Spleen	Spleen
10	chr1:225946600-225955400	Weak transcription	Fetal Intestine Large	intestine
11	chr1:225948800-225952200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:225949200-225951400	Enhancers	Osteobl	bone
13	chr1:225949400-225950600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr1:225949400-225950800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:225949400-225950800	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr1:225949400-225950800	Enhancers	NHLF	lung
17	chr1:225949400-225952000	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr1:225949400-225952200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr1:225949400-225952400	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr1:225949400-225952600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr1:225949600-225950600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:225949600-225950600	Enhancers	H9 Cell Line	embryonic stem cell
23	chr1:225949600-225950600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr1:225949600-225950600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr1:225949600-225950600	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr1:225949600-225950600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:225949600-225950600	Enhancers	Fetal Heart	heart
28	chr1:225949600-225950600	Enhancers	HSMM	muscle
29	chr1:225949600-225950600	Flanking Active TSS	NH-A	brain
30	chr1:225949600-225950800	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr1:225949600-225950800	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr1:225949600-225950800	Enhancers	Right Atrium	heart
33	chr1:225949600-225951000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:225949600-225951400	Enhancers	HUVEC	blood vessel
35	chr1:225949600-225951600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:225949600-225951600	Enhancers	Adipose Nuclei	Adipose
37	chr1:225949600-225951600	Enhancers	Colon Smooth Muscle	Colon
38	chr1:225949600-225951800	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr1:225949600-225952200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:225949600-225952200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr1:225949600-225952200	Enhancers	Left Ventricle	heart
42	chr1:225949600-225952200	Enhancers	Ovary	ovary
43	chr1:225949600-225952400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:225949600-225952400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:225949600-225952400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:225949600-225952800	Enhancers	Fetal Muscle Trunk	muscle
47	chr1:225949600-225954000	Enhancers	Fetal Lung	lung
48	chr1:225949600-225960400	Enhancers	Fetal Muscle Leg	muscle
49	chr1:225949800-225950600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr1:225949800-225950600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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