Variant report

Variant	rs9291133
Chromosome Location	chr4:7256620-7256621
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10022730	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10025225	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10032667	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11730548	0.83[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4376139	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4527475	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4610334	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4689669	0.85[ASN][1000 genomes]
rs6446588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6812479	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6815971	0.92[ASN][1000 genomes]
rs6841241	0.94[ASN][1000 genomes]
rs6843561	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6847479	0.91[ASN][1000 genomes]
rs7436907	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7441995	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7661994	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34033	chr4:6973270-7390621	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv2757919	chr4:6988148-7269901	Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv2759221	chr4:6988148-7269901	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv428436	chr4:6988148-7269901	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	nsv829850	chr4:7112509-7314016	Bivalent Enhancer Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
6	nsv432556	chr4:7174993-7391948	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
7	nsv878541	chr4:7211197-7341243	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv878542	chr4:7214696-7276541	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv461198	chr4:7219933-7265635	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv593565	chr4:7219933-7265635	ZNF genes & repeats Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv4218	chr4:7225196-7270057	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv916610	chr4:7238883-7731946	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
13	nsv461199	chr4:7253260-7270126	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv593566	chr4:7253260-7270126	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv461200	chr4:7256620-7297506	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv593567	chr4:7256620-7297506	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
17	nsv461201	chr4:7256620-7311399	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
18	nsv593568	chr4:7256620-7311399	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9291133	JAKMIP1	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:7252600-7261800	Weak transcription	Fetal Brain Female	brain
2	chr4:7252600-7262400	Weak transcription	Fetal Brain Male	brain
3	chr4:7252800-7256800	Weak transcription	HSMMtube	muscle
4	chr4:7252800-7257800	Weak transcription	Ovary	ovary
5	chr4:7253000-7257200	Weak transcription	Psoas Muscle	Psoas
6	chr4:7253000-7265400	Weak transcription	Brain Substantia Nigra	brain
7	chr4:7253400-7258000	Weak transcription	Colon Smooth Muscle	Colon
8	chr4:7253600-7258000	Weak transcription	Brain Hippocampus Middle	brain
9	chr4:7253600-7258200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr4:7253600-7258400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr4:7253800-7258200	Weak transcription	Brain Angular Gyrus	brain
12	chr4:7254000-7256800	Weak transcription	Esophagus	oesophagus
13	chr4:7254000-7259200	Weak transcription	Spleen	Spleen
14	chr4:7254200-7258200	Enhancers	Fetal Heart	heart
15	chr4:7254600-7258200	Weak transcription	Duodenum Smooth Muscle	Duodenum
16	chr4:7254800-7258200	Weak transcription	Fetal Lung	lung
17	chr4:7255200-7262800	Weak transcription	Brain Germinal Matrix	brain
18	chr4:7255400-7257400	Enhancers	GM12878-XiMat	blood
19	chr4:7255400-7259000	Enhancers	HSMM	muscle
20	chr4:7255400-7259800	Enhancers	Fetal Muscle Leg	muscle
21	chr4:7255600-7257800	Weak transcription	Right Atrium	heart
22	chr4:7255600-7258800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr4:7256000-7257000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr4:7256200-7257000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr4:7256200-7257000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr4:7256200-7257600	Enhancers	Fetal Muscle Trunk	muscle
27	chr4:7256400-7257000	Enhancers	Fetal Thymus	thymus
28	chr4:7256400-7257400	Enhancers	Brain Anterior Caudate	brain
29	chr4:7256400-7259800	Enhancers	Left Ventricle	heart
30	chr4:7256600-7257000	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr4:7256600-7257000	Enhancers	Lung	lung
32	chr4:7256600-7257200	Enhancers	Stomach Smooth Muscle	stomach
33	chr4:7256600-7258400	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr4:7256600-7258600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr4:7256600-7259600	Enhancers	Right Ventricle	heart
36	chr4:7256600-7259800	Enhancers	Skeletal Muscle Female	skeletal muscle

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