Variant report

Variant	rs11740402
Chromosome Location	chr5:58537849-58537850
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10036406	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10038599	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs10055446	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10059709	1.00[ASW][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10061600	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10061786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10064893	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10068836	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10070294	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10070436	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10075364	0.98[ASN][1000 genomes]
rs10440630	0.83[CEU][hapmap];0.89[CHB][hapmap];0.89[CHD][hapmap];0.87[GIH][hapmap]
rs11738043	1.00[ASW][hapmap]
rs11747413	0.91[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13328160	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap]
rs13328226	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs13356883	1.00[ASW][hapmap]
rs13360907	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17444059	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17528257	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17528285	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17528473	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17780213	1.00[MEX][hapmap];0.87[TSI][hapmap]
rs1824159	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs2112959	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs28529077	0.98[ASN][1000 genomes]
rs28647633	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57516309	0.81[AMR][1000 genomes]
rs60453299	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881054	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs72765932	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72765942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72765953	0.98[ASN][1000 genomes]
rs72765961	0.98[ASN][1000 genomes]
rs72765993	0.81[AMR][1000 genomes]
rs9292206	1.00[ASW][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2830363	chr5:57893949-58555491	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1023570	chr5:58486384-58537849	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv598252	chr5:58487764-58618889	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv881703	chr5:58517918-58540847	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1025807	chr5:58520050-58548231	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv520721	chr5:58520735-58558388	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11740402	IPO11	cis	parietal	SCAN
rs11740402	ZNF266	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58527400-58549800	Weak transcription	Aorta	Aorta
2	chr5:58532600-58540800	Weak transcription	Fetal Muscle Leg	muscle
3	chr5:58532600-58541000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr5:58533200-58540800	Weak transcription	HSMMtube	muscle
5	chr5:58533600-58541000	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr5:58533800-58538400	Enhancers	A549	lung
7	chr5:58534000-58538000	Weak transcription	Small Intestine	intestine
8	chr5:58535200-58538800	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr5:58535400-58539000	Enhancers	Colon Smooth Muscle	Colon
10	chr5:58535400-58541000	Weak transcription	Fetal Intestine Large	intestine
11	chr5:58535600-58540800	Weak transcription	Brain Hippocampus Middle	brain
12	chr5:58535600-58540800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:58535600-58541000	Weak transcription	Right Ventricle	heart
14	chr5:58535600-58551800	Weak transcription	HUVEC	blood vessel
15	chr5:58537000-58538600	Enhancers	Rectal Smooth Muscle	rectum
16	chr5:58537200-58538000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr5:58537200-58538000	Weak transcription	Psoas Muscle	Psoas
18	chr5:58537200-58540800	Weak transcription	Fetal Intestine Small	intestine
19	chr5:58537200-58540800	Weak transcription	Right Atrium	heart
20	chr5:58537200-58541000	Weak transcription	Osteobl	bone
21	chr5:58537200-58541400	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr5:58537200-58542600	Weak transcription	Fetal Kidney	kidney
23	chr5:58537400-58540800	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:58537400-58541000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr5:58537400-58542200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr5:58537400-58543600	Weak transcription	Left Ventricle	heart
27	chr5:58537600-58538600	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr5:58537600-58540800	Weak transcription	Brain Angular Gyrus	brain
29	chr5:58537600-58541000	Weak transcription	Fetal Heart	heart
30	chr5:58537600-58548600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr5:58537600-58553000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr5:58537800-58540800	Weak transcription	Adipose Nuclei	Adipose
33	chr5:58537800-58541000	Weak transcription	Brain Substantia Nigra	brain
34	chr5:58537800-58542600	Weak transcription	Hela-S3	cervix

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