Variant report

Variant	rs10038599
Chromosome Location	chr5:58554405-58554406
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10036406	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10055446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10059709	0.88[CHB][hapmap];0.92[JPT][hapmap]
rs10061600	0.85[ASN][1000 genomes]
rs10061786	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10064893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10068836	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs10070294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10070436	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10075364	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10079396	0.80[CEU][hapmap]
rs10440630	0.89[CHB][hapmap]
rs11740402	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs11747413	0.85[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs13328160	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13328175	0.84[CEU][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13328226	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13354210	0.85[CEU][hapmap]
rs17444059	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17528257	0.84[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap]
rs17528285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17528473	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17528634	0.85[CEU][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17780213	0.81[CEU][hapmap]
rs17780740	0.84[CEU][hapmap]
rs2112959	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2194210	0.80[CEU][hapmap]
rs28529077	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61683381	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6881054	1.00[CHB][hapmap];0.80[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72765932	0.89[ASN][1000 genomes]
rs72765953	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72765961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72765990	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9292201	0.84[CEU][hapmap];0.88[EUR][1000 genomes]
rs9686434	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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
3	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

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58541200-58558400	Weak transcription	Pancreas	Pancrea
2	chr5:58541600-58560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr5:58541600-58562400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr5:58541800-58562800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr5:58549000-58555200	Weak transcription	Hela-S3	cervix
6	chr5:58551400-58557600	Enhancers	Rectal Smooth Muscle	rectum
7	chr5:58552200-58556800	Weak transcription	Brain Substantia Nigra	brain
8	chr5:58552400-58555200	Enhancers	Colon Smooth Muscle	Colon
9	chr5:58552400-58555200	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr5:58552400-58558400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:58552600-58556600	Weak transcription	Brain Angular Gyrus	brain
12	chr5:58552600-58560400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:58553200-58555000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr5:58553400-58560000	Weak transcription	Fetal Lung	lung
15	chr5:58553600-58556600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:58553800-58558400	Weak transcription	Left Ventricle	heart
17	chr5:58553800-58558400	Weak transcription	Right Atrium	heart
18	chr5:58553800-58568600	Weak transcription	Fetal Muscle Leg	muscle
19	chr5:58554200-58554800	Active TSS	A549	lung
20	chr5:58554200-58555200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr5:58554200-58556800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:58554200-58556800	Weak transcription	Fetal Intestine Large	intestine
23	chr5:58554200-58556800	Weak transcription	Fetal Intestine Small	intestine
24	chr5:58554200-58556800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr5:58554200-58557000	Weak transcription	Fetal Kidney	kidney
26	chr5:58554200-58558400	Weak transcription	Psoas Muscle	Psoas
27	chr5:58554200-58559600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr5:58554200-58561000	Weak transcription	Stomach Mucosa	stomach
29	chr5:58554200-58562600	Weak transcription	Duodenum Mucosa	Duodenum
30	chr5:58554400-58554800	Weak transcription	Fetal Heart	heart
31	chr5:58554400-58555000	Weak transcription	HSMMtube	muscle
32	chr5:58554400-58558400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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