Variant report

Variant	rs2668549
Chromosome Location	chr4:54514353-54514354
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1079230	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1107027	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1477875	0.89[ASN][1000 genomes]
rs1477876	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1546526	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1972815	0.89[CEU][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1996005	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2164266	0.91[ASN][1000 genomes]
rs2572283	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2572291	0.89[ASN][1000 genomes]
rs2572299	0.89[ASN][1000 genomes]
rs2590780	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2590781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2590816	0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.90[TSI][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2590823	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2616386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668516	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2668521	0.89[ASN][1000 genomes]
rs2668524	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668529	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2668548	0.87[EUR][1000 genomes]
rs2668557	0.85[EUR][1000 genomes]
rs2668566	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7686480	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829936	chr4:54367783-54556123	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2668549	TXNDC9	cis	parietal	SCAN
rs2668549	FIP1L1	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:54507800-54517000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr4:54507800-54520600	Weak transcription	Gastric	stomach
3	chr4:54508000-54519200	Weak transcription	Fetal Heart	heart
4	chr4:54511400-54515600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:54511400-54515800	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr4:54511400-54517200	Weak transcription	NHEK	skin
7	chr4:54511400-54520600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:54511600-54514800	Weak transcription	Left Ventricle	heart
9	chr4:54511600-54515600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:54511600-54515600	Weak transcription	Esophagus	oesophagus
11	chr4:54511600-54517400	Weak transcription	Lung	lung
12	chr4:54511600-54518800	Weak transcription	Liver	Liver
13	chr4:54511800-54515800	Weak transcription	Placenta	Placenta
14	chr4:54511800-54515800	Weak transcription	Right Atrium	heart
15	chr4:54511800-54516000	Weak transcription	Right Ventricle	heart
16	chr4:54511800-54518400	Weak transcription	GM12878-XiMat	blood
17	chr4:54512000-54517400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr4:54512200-54517000	Weak transcription	Fetal Intestine Small	intestine
19	chr4:54512600-54515800	Weak transcription	Psoas Muscle	Psoas
20	chr4:54512600-54518600	Weak transcription	Colonic Mucosa	Colon
21	chr4:54513400-54515600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr4:54513400-54515800	Weak transcription	Adipose Nuclei	Adipose
23	chr4:54513400-54515800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:54513400-54515800	Weak transcription	Fetal Intestine Large	intestine
25	chr4:54513400-54515800	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr4:54513400-54516200	Weak transcription	Pancreas	Pancrea
27	chr4:54513400-54519600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr4:54513600-54515800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr4:54513800-54515600	Weak transcription	Stomach Mucosa	stomach
30	chr4:54514000-54516800	Weak transcription	Small Intestine	intestine

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