Variant report

Variant	rs16889495
Chromosome Location	chr5:58558388-58558389
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10038855	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10039990	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10045441	0.84[ASN][1000 genomes]
rs10055869	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs10072367	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13169097	1.00[CHB][hapmap]
rs13354612	0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs154221	0.83[TSI][hapmap]
rs16889508	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16889512	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17528543	0.83[TSI][hapmap]
rs17528550	0.83[TSI][hapmap]
rs2306292	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4618401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292199	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9292200	1.00[CHB][hapmap];1.00[JPT][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	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
2	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
3	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

No data

Chromatin state (count:28 , 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	chr5:58552400-58558400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:58552600-58560400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:58553400-58560000	Weak transcription	Fetal Lung	lung
8	chr5:58553800-58558400	Weak transcription	Left Ventricle	heart
9	chr5:58553800-58558400	Weak transcription	Right Atrium	heart
10	chr5:58553800-58568600	Weak transcription	Fetal Muscle Leg	muscle
11	chr5:58554200-58558400	Weak transcription	Psoas Muscle	Psoas
12	chr5:58554200-58559600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr5:58554200-58561000	Weak transcription	Stomach Mucosa	stomach
14	chr5:58554200-58562600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr5:58554400-58558400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:58555800-58558600	Enhancers	Colon Smooth Muscle	Colon
17	chr5:58556200-58558400	Weak transcription	Fetal Heart	heart
18	chr5:58556800-58558600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr5:58557000-58559200	Weak transcription	Hela-S3	cervix
20	chr5:58557200-58560000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:58557200-58560600	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr5:58557200-58562400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr5:58557400-58560600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:58558000-58558800	Enhancers	Rectal Smooth Muscle	rectum
25	chr5:58558000-58560600	Weak transcription	Fetal Intestine Large	intestine
26	chr5:58558000-58561000	Weak transcription	Fetal Intestine Small	intestine
27	chr5:58558200-58558600	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr5:58558200-58559000	Transcr. at gene 5' and 3'	A549	lung

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