Variant report

Variant	rs1589241
Chromosome Location	chr4:142565089-142565090
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10028670	0.90[EUR][1000 genomes]
rs1040257	0.95[CEU][hapmap];0.90[EUR][1000 genomes]
rs11100722	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100723	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100724	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12508955	0.95[CEU][hapmap];0.86[EUR][1000 genomes]
rs13111860	0.87[EUR][1000 genomes]
rs1476326	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493024	0.86[EUR][1000 genomes]
rs1519550	0.86[EUR][1000 genomes]
rs1519552	0.95[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1519553	0.95[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs1607592	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1607593	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1850853	0.90[EUR][1000 genomes]
rs2087849	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs2254514	0.87[EUR][1000 genomes]
rs2322262	0.95[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4956404	0.95[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs4956407	0.95[CEU][hapmap];0.87[EUR][1000 genomes]
rs6537058	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6816210	0.95[CEU][hapmap];0.92[YRI][hapmap];0.84[EUR][1000 genomes]
rs6837991	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6841454	0.95[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs6842194	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7661408	0.86[EUR][1000 genomes]
rs7665842	0.84[EUR][1000 genomes]
rs7688250	0.95[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs7698675	0.95[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9683566	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9684235	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970327	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs970328	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs990851	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880172	chr4:142355535-142565089	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv880173	chr4:142355535-142666106	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830094	chr4:142411738-142567788	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv3401979	chr4:142434442-142803321	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1018949	chr4:142451823-142732365	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1030822	chr4:142487721-142706053	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv1027004	chr4:142487721-143007320	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1589241	MED9	trans	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142558600-142569000	Weak transcription	Small Intestine	intestine
2	chr4:142559800-142574000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr4:142560000-142575200	Weak transcription	Right Atrium	heart
4	chr4:142561400-142567600	Weak transcription	Colon Smooth Muscle	Colon
5	chr4:142562200-142568600	Weak transcription	Primary B cells from peripheral blood	blood
6	chr4:142563400-142565200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr4:142563400-142565200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr4:142563400-142565400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:142563400-142565400	Enhancers	Sigmoid Colon	Sigmoid Colon
10	chr4:142563400-142565400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr4:142563400-142565400	Enhancers	Hela-S3	cervix
12	chr4:142563400-142565600	Enhancers	NHEK	skin
13	chr4:142563400-142565800	Enhancers	HSMM	muscle
14	chr4:142563400-142566000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr4:142563400-142568600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:142563400-142569200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr4:142563400-142569200	Enhancers	Osteobl	bone
18	chr4:142563400-142569400	Enhancers	HMEC	breast
19	chr4:142563400-142569600	Enhancers	NHDF-Ad	bronchial
20	chr4:142563600-142565200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr4:142563600-142565200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
22	chr4:142563600-142565400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:142563600-142565400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr4:142563600-142565400	Enhancers	NHLF	lung
25	chr4:142563600-142565800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr4:142563600-142565800	Enhancers	NH-A	brain
27	chr4:142563800-142565200	Enhancers	HUVEC	blood vessel
28	chr4:142563800-142565400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr4:142563800-142565600	Active TSS	GM12878-XiMat	blood
30	chr4:142563800-142566600	Weak transcription	Aorta	Aorta
31	chr4:142563800-142568600	Weak transcription	Adipose Nuclei	Adipose
32	chr4:142564000-142568800	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr4:142564000-142568800	Weak transcription	Spleen	Spleen
34	chr4:142564000-142569200	Weak transcription	Esophagus	oesophagus
35	chr4:142564000-142575200	Weak transcription	Psoas Muscle	Psoas
36	chr4:142564200-142569000	Weak transcription	Monocytes-CD14+_RO01746	blood
37	chr4:142564400-142565200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr4:142564400-142565400	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr4:142564400-142565600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr4:142564600-142565200	Enhancers	Fetal Stomach	stomach
41	chr4:142564600-142565200	Enhancers	HSMMtube	muscle
42	chr4:142564600-142570200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr4:142565000-142568800	Enhancers	A549	lung

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