Variant report

Variant	rs1558572
Chromosome Location	chr4:15538744-15538745
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1125378	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12500587	0.84[CHD][hapmap]
rs4235379	0.81[CHD][hapmap];0.84[JPT][hapmap]
rs6811445	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6812708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7696938	0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer 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	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1558572	CC2D2A	cis	parietal	SCAN
rs1558572	FBXL5	Cis_1M	lymphoblastoid	RTeQTL
rs1558572	FAM200B	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15487400-15570400	Weak transcription	Psoas Muscle	Psoas
2	chr4:15490400-15539600	Weak transcription	Esophagus	oesophagus
3	chr4:15495600-15559400	Weak transcription	HSMMtube	muscle
4	chr4:15502000-15539400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr4:15502400-15539400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:15502800-15549200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr4:15502800-15577600	Weak transcription	Right Ventricle	heart
8	chr4:15508200-15556400	Weak transcription	Colonic Mucosa	Colon
9	chr4:15508800-15545800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr4:15509200-15564400	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:15509600-15553400	Weak transcription	HepG2	liver
12	chr4:15512000-15580000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr4:15513000-15562400	Weak transcription	Primary B cells from cord blood	blood
14	chr4:15515400-15545200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr4:15516000-15545600	Weak transcription	Fetal Thymus	thymus
16	chr4:15517800-15551600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:15517800-15593600	Weak transcription	HUVEC	blood vessel
18	chr4:15519400-15539600	Weak transcription	Gastric	stomach
19	chr4:15519800-15539600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr4:15520000-15572400	Weak transcription	Small Intestine	intestine
21	chr4:15520400-15539000	Weak transcription	NHLF	lung
22	chr4:15520400-15544200	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr4:15520600-15539200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr4:15520600-15539400	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr4:15520600-15544400	Weak transcription	H1 Cell Line	embryonic stem cell
26	chr4:15520600-15544600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr4:15520600-15545200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr4:15520600-15553400	Weak transcription	A549	lung
29	chr4:15520800-15539800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr4:15520800-15545000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr4:15521800-15539600	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:15522200-15544600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr4:15523800-15539200	Weak transcription	Fetal Intestine Large	intestine
34	chr4:15524000-15539200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr4:15526000-15558200	Weak transcription	Spleen	Spleen
36	chr4:15527600-15539600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr4:15527800-15539400	Weak transcription	HMEC	breast
38	chr4:15529200-15538800	Weak transcription	Pancreas	Pancrea
39	chr4:15530200-15556600	Weak transcription	HSMM	muscle
40	chr4:15530600-15540000	Weak transcription	NHDF-Ad	bronchial
41	chr4:15530800-15539200	Weak transcription	Left Ventricle	heart
42	chr4:15530800-15539400	Weak transcription	Osteobl	bone
43	chr4:15530800-15554600	Weak transcription	Placenta	Placenta
44	chr4:15530800-15554600	Weak transcription	NH-A	brain
45	chr4:15531000-15539600	Weak transcription	Aorta	Aorta
46	chr4:15531000-15539800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr4:15531200-15538800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:15531200-15539200	Weak transcription	Brain Inferior Temporal Lobe	brain
49	chr4:15531200-15539400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:15531200-15539400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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