Variant report

Variant	rs1445948
Chromosome Location	chr5:58542222-58542223
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1031197	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10491352	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10940644	1.00[JPT][hapmap]
rs11954668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11959132	1.00[JPT][hapmap]
rs11959567	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs12519611	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1445952	0.81[ASN][1000 genomes]
rs1445953	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1445954	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1471429	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1471430	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16889479	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs16889499	0.86[ASN][1000 genomes]
rs16889518	0.81[ASN][1000 genomes]
rs17444185	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17528522	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs17528578	0.81[ASN][1000 genomes]
rs17628114	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17780175	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1823070	0.86[ASN][1000 genomes]
rs1824157	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1838733	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1867711	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1867712	0.86[ASN][1000 genomes]
rs1947090	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2021775	1.00[JPT][hapmap]
rs2028836	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2081106	1.00[JPT][hapmap]
rs2409631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28862729	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4700325	1.00[JPT][hapmap]
rs4700327	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4700328	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs67196739	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67526430	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6858946	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6877508	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs6888028	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891161	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6897568	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs765182	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7703022	1.00[CHB][hapmap]
rs7717303	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719441	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
4	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:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58527400-58549800	Weak transcription	Aorta	Aorta
2	chr5:58535600-58551800	Weak transcription	HUVEC	blood vessel
3	chr5:58537200-58542600	Weak transcription	Fetal Kidney	kidney
4	chr5:58537400-58543600	Weak transcription	Left Ventricle	heart
5	chr5:58537600-58548600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr5:58537600-58553000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr5:58537800-58542600	Weak transcription	Hela-S3	cervix
8	chr5:58539000-58543000	Weak transcription	Small Intestine	intestine
9	chr5:58540800-58542800	Enhancers	Brain Angular Gyrus	brain
10	chr5:58540800-58543000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:58540800-58543200	Enhancers	Colon Smooth Muscle	Colon
12	chr5:58540800-58543800	Enhancers	Fetal Lung	lung
13	chr5:58541000-58543000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr5:58541000-58543400	Enhancers	Osteobl	bone
15	chr5:58541000-58545400	Enhancers	Rectal Smooth Muscle	rectum
16	chr5:58541200-58543200	Enhancers	Pancreatic Islets	Pancreatic Islet
17	chr5:58541200-58558400	Weak transcription	Pancreas	Pancrea
18	chr5:58541400-58543200	Enhancers	Muscle Satellite Cultured Cells	--
19	chr5:58541600-58542800	Weak transcription	Brain Substantia Nigra	brain
20	chr5:58541600-58560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr5:58541600-58562400	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr5:58541800-58542800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr5:58541800-58542800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr5:58541800-58543200	Weak transcription	Fetal Intestine Large	intestine
25	chr5:58541800-58543400	Weak transcription	Fetal Intestine Small	intestine
26	chr5:58541800-58543400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:58541800-58543600	Weak transcription	Psoas Muscle	Psoas
28	chr5:58541800-58543600	Weak transcription	Right Atrium	heart
29	chr5:58541800-58562800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr5:58542000-58542400	Weak transcription	Stomach Smooth Muscle	stomach
31	chr5:58542000-58543200	Flanking Active TSS	A549	lung
32	chr5:58542200-58542600	Enhancers	Brain Cingulate Gyrus	brain
33	chr5:58542200-58544400	Enhancers	Fetal Heart	heart
34	chr5:58542200-58551600	Weak transcription	Primary neutrophils fromperipheralblood	blood

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