Variant report

Variant	rs455969
Chromosome Location	chr5:58558410-58558411
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs153985	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs181915	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs255557	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs26689	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs26694	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs26700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26703	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs26710	0.91[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs26713	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs26714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs26715	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27549	0.84[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27670	0.88[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs27695	0.88[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs27773	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs27957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28055	0.85[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35304	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35308	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35310	0.88[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs466742	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58541600-58560000	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr5:58541600-58562400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr5:58541800-58562800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:58552600-58560400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:58553400-58560000	Weak transcription	Fetal Lung	lung
6	chr5:58553800-58568600	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:58554200-58559600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr5:58554200-58561000	Weak transcription	Stomach Mucosa	stomach
9	chr5:58554200-58562600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr5:58555800-58558600	Enhancers	Colon Smooth Muscle	Colon
11	chr5:58556800-58558600	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr5:58557000-58559200	Weak transcription	Hela-S3	cervix
13	chr5:58557200-58560000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:58557200-58560600	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr5:58557200-58562400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr5:58557400-58560600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:58558000-58558800	Enhancers	Rectal Smooth Muscle	rectum
18	chr5:58558000-58560600	Weak transcription	Fetal Intestine Large	intestine
19	chr5:58558000-58561000	Weak transcription	Fetal Intestine Small	intestine
20	chr5:58558200-58558600	Enhancers	Skeletal Muscle Female	skeletal muscle
21	chr5:58558200-58559000	Transcr. at gene 5' and 3'	A549	lung
22	chr5:58558400-58558600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr5:58558400-58558600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:58558400-58559200	Enhancers	Aorta	Aorta
25	chr5:58558400-58559200	Enhancers	Left Ventricle	heart
26	chr5:58558400-58559200	Enhancers	Pancreas	Pancrea
27	chr5:58558400-58559200	Enhancers	Psoas Muscle	Psoas
28	chr5:58558400-58559200	Enhancers	Right Atrium	heart
29	chr5:58558400-58564400	Enhancers	Fetal Heart	heart

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