Variant report

Variant	rs16889682
Chromosome Location	chr5:58648408-58648409
allele	A/C
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:34)

rs_ID	r²[population]
rs10514864	1.00[CEU][hapmap]
rs10514865	1.00[CHB][hapmap]
rs12658429	1.00[CEU][hapmap]
rs13164719	0.85[ASN][1000 genomes]
rs1445947	1.00[CEU][hapmap]
rs1457110	1.00[CEU][hapmap]
rs154223	1.00[CEU][hapmap]
rs16889611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16889696	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16889743	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16889796	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs16889846	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17589745	1.00[CEU][hapmap]
rs27185	1.00[CEU][hapmap]
rs27532	1.00[CEU][hapmap]
rs56874033	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61021367	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450516	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6450518	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872808	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6888644	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6889851	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6895550	1.00[JPT][hapmap]
rs6895685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6898269	1.00[CEU][hapmap]
rs73092919	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73092930	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73092991	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73095430	1.00[EUR][1000 genomes]
rs7700870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7703702	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs7733716	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7735133	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7736808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1030716	chr5:58636116-58718362	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1032732	chr5:58637179-58689010	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1022160	chr5:58645805-58689010	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58635200-58652600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr5:58642200-58653200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:58642600-58652600	Weak transcription	Fetal Brain Male	brain
4	chr5:58642600-58652600	Weak transcription	Small Intestine	intestine
5	chr5:58643600-58652400	Weak transcription	Fetal Kidney	kidney
6	chr5:58644200-58650400	Enhancers	Fetal Heart	heart
7	chr5:58644800-58648600	Weak transcription	Hela-S3	cervix
8	chr5:58646200-58654400	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr5:58646600-58648600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr5:58646600-58649400	Enhancers	Brain Substantia Nigra	brain
11	chr5:58646600-58649400	Enhancers	Duodenum Smooth Muscle	Duodenum
12	chr5:58646600-58650000	Enhancers	Fetal Lung	lung
13	chr5:58646800-58648600	Enhancers	Brain Angular Gyrus	brain
14	chr5:58647000-58648600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr5:58647000-58648800	Enhancers	Brain Anterior Caudate	brain
16	chr5:58647000-58649000	Enhancers	Fetal Stomach	stomach
17	chr5:58647200-58650400	Enhancers	Rectal Smooth Muscle	rectum
18	chr5:58647600-58648600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:58647800-58648600	Enhancers	Right Ventricle	heart
20	chr5:58647800-58649000	Enhancers	Stomach Mucosa	stomach
21	chr5:58648000-58648600	Enhancers	Stomach Smooth Muscle	stomach
22	chr5:58648000-58649000	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr5:58648000-58649400	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr5:58648000-58649400	Weak transcription	Right Atrium	heart
25	chr5:58648000-58650600	Enhancers	Colon Smooth Muscle	Colon
26	chr5:58648000-58652600	Weak transcription	Fetal Muscle Leg	muscle
27	chr5:58648000-58654200	Weak transcription	Ovary	ovary
28	chr5:58648200-58648800	Transcr. at gene 5' and 3'	A549	lung
29	chr5:58648200-58650400	Enhancers	Adipose Nuclei	Adipose
30	chr5:58648200-58652200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr5:58648200-58652200	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr5:58648400-58648800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr5:58648400-58649400	Weak transcription	Psoas Muscle	Psoas
34	chr5:58648400-58649400	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr5:58648400-58650400	Weak transcription	Left Ventricle	heart
36	chr5:58648400-58652400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr5:58648400-58652600	Weak transcription	Brain Hippocampus Middle	brain

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