Variant report

Variant	rs10036406
Chromosome Location	chr5:58552313-58552314
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10038599	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10055446	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10059709	0.88[CHB][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10060200	0.91[CEU][hapmap]
rs10061600	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10061786	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs10064893	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10068836	0.91[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10070294	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs10070436	0.91[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];0.98[ASN][1000 genomes]
rs10075364	0.90[ASN][1000 genomes]
rs10079396	0.88[CEU][hapmap]
rs10079614	0.84[EUR][1000 genomes]
rs10440630	0.89[CHB][hapmap]
rs11740402	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]
rs11747413	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13328160	0.91[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs13328175	0.81[CEU][hapmap]
rs13328226	0.91[CEU][hapmap];1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs13354210	0.82[CEU][hapmap]
rs13360907	0.87[ASN][1000 genomes]
rs17444059	0.83[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs17528257	0.81[CEU][hapmap];1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs17528285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs17528473	0.91[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs17528634	0.82[CEU][hapmap];1.00[AFR][1000 genomes]
rs17724250	0.91[CEU][hapmap]
rs17780213	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs17780584	0.90[CEU][hapmap];1.00[AFR][1000 genomes]
rs17780740	0.82[CEU][hapmap]
rs1824159	0.90[CEU][hapmap]
rs2044419	0.84[EUR][1000 genomes]
rs2112959	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs2194210	0.89[CEU][hapmap]
rs28529077	0.90[ASN][1000 genomes]
rs28647633	0.87[ASN][1000 genomes]
rs55837553	1.00[AFR][1000 genomes]
rs56183128	0.84[EUR][1000 genomes]
rs57516309	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60453299	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6881054	1.00[CHB][hapmap];0.90[ASN][1000 genomes]
rs72765932	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72765942	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72765953	0.90[ASN][1000 genomes]
rs72765961	0.90[ASN][1000 genomes]
rs72765990	1.00[AFR][1000 genomes]
rs72765993	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72767710	0.84[EUR][1000 genomes]
rs9292201	0.81[CEU][hapmap]

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:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58537600-58553000	Weak transcription	Duodenum Mucosa	Duodenum
2	chr5:58541200-58558400	Weak transcription	Pancreas	Pancrea
3	chr5:58541600-58560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr5:58541600-58562400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:58541800-58562800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:58543200-58552400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr5:58544400-58553000	Weak transcription	Left Ventricle	heart
8	chr5:58546400-58552400	Weak transcription	Psoas Muscle	Psoas
9	chr5:58549000-58553800	Weak transcription	Stomach Mucosa	stomach
10	chr5:58549000-58555200	Weak transcription	Hela-S3	cervix
11	chr5:58549800-58553200	Enhancers	Pancreatic Islets	Pancreatic Islet
12	chr5:58550400-58553200	Weak transcription	HepG2	liver
13	chr5:58551400-58554200	Enhancers	Fetal Kidney	kidney
14	chr5:58551400-58557600	Enhancers	Rectal Smooth Muscle	rectum
15	chr5:58551600-58552400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr5:58551600-58552600	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr5:58551600-58552600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr5:58551600-58552800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:58551600-58553200	Enhancers	Primary hematopoietic stem cells short term culture	blood
20	chr5:58551600-58553600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:58551600-58553600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:58551800-58552400	Enhancers	HUVEC	blood vessel
23	chr5:58551800-58552600	Enhancers	Brain Angular Gyrus	brain
24	chr5:58551800-58552600	Enhancers	Brain Hippocampus Middle	brain
25	chr5:58551800-58552800	Enhancers	Fetal Lung	lung
26	chr5:58551800-58554200	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr5:58551800-58554200	Flanking Active TSS	A549	lung
28	chr5:58552000-58552400	Flanking Active TSS	Colon Smooth Muscle	Colon
29	chr5:58552000-58552600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:58552000-58552600	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr5:58552000-58553000	Enhancers	Brain Cingulate Gyrus	brain
32	chr5:58552200-58552400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:58552200-58552400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr5:58552200-58552400	Enhancers	Fetal Heart	heart
35	chr5:58552200-58552400	Enhancers	Fetal Intestine Large	intestine
36	chr5:58552200-58552600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr5:58552200-58552600	Enhancers	Fetal Stomach	stomach
38	chr5:58552200-58556800	Weak transcription	Brain Substantia Nigra	brain

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