Variant report

Variant	rs549280
Chromosome Location	chr4:74971196-74971197
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	chr4:74969971..74972171-chr4:74976711..74978462,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10938107	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];0.89[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11725704	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11733208	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12642974	0.95[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12649753	0.87[ASN][1000 genomes]
rs13124617	0.83[EUR][1000 genomes]
rs1371794	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1371798	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs1371799	0.91[CEU][hapmap];0.94[EUR][1000 genomes]
rs1837559	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1866755	0.91[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs3806792	0.91[CEU][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs4121652	0.92[EUR][1000 genomes]
rs518867	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs546829	0.90[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72652928	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72652934	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7667376	0.84[CEU][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes]
rs7686861	0.87[CEU][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs882638	0.87[CEU][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs9131	0.87[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs981458	0.89[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	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1004768	chr4:74774372-75109579	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1006218	chr4:74782324-75105424	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1006029	chr4:74793922-74986664	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs549280	UTP3	cis	parietal	SCAN
rs549280	CCNG2	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:74965400-74971200	Weak transcription	Stomach Mucosa	stomach
2	chr4:74965600-74971200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr4:74965600-74971400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:74965600-74974800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:74966000-74971200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr4:74966000-74971800	Enhancers	Liver	Liver
7	chr4:74966000-74973000	Weak transcription	HUVEC	blood vessel
8	chr4:74966200-74971200	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:74966200-74971600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr4:74966200-74975000	Enhancers	Hela-S3	cervix
11	chr4:74966400-74971400	Weak transcription	HSMM	muscle
12	chr4:74966400-74971600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr4:74966400-74971600	Weak transcription	NHDF-Ad	bronchial
14	chr4:74966400-74972800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:74966400-74973600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:74966400-74974400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr4:74966800-74978000	Weak transcription	Gastric	stomach
18	chr4:74968200-74973400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:74968200-74973400	Weak transcription	NHEK	skin
20	chr4:74968400-74971400	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr4:74968400-74974600	Weak transcription	K562	blood
22	chr4:74968600-74974000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr4:74968800-74971400	Weak transcription	Osteobl	bone
24	chr4:74969000-74971200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:74969000-74974200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr4:74969400-74971600	Weak transcription	Pancreas	Pancrea
27	chr4:74969400-74972000	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr4:74969600-74972800	Enhancers	Fetal Intestine Large	intestine
29	chr4:74969800-74972200	Enhancers	Rectal Mucosa Donor 31	rectum
30	chr4:74970200-74971200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr4:74970200-74971600	Weak transcription	Right Atrium	heart
32	chr4:74970200-74975000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr4:74970400-74971400	Weak transcription	A549	lung
34	chr4:74970800-74971200	Weak transcription	Fetal Intestine Small	intestine

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