Variant report

Variant	rs40122
Chromosome Location	chr5:58628717-58628718
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs154024	0.92[CEU][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs154031	0.92[EUR][1000 genomes]
rs193447	0.80[GIH][hapmap]
rs244573	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs244574	0.89[CHB][hapmap]
rs244577	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs244587	1.00[GIH][hapmap]
rs35258	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs35261	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35267	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs35274	0.89[ASW][hapmap]
rs35276	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35278	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35279	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35283	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35284	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.89[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs39672	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs40328	0.85[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]

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	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	nsv1030117	chr5:58587672-58637179	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58618800-58629000	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr5:58624600-58630000	Weak transcription	Fetal Intestine Small	intestine
3	chr5:58625000-58632000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:58625000-58632400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:58625000-58632400	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr5:58625000-58644600	Weak transcription	Left Ventricle	heart
7	chr5:58625400-58630800	Weak transcription	Colon Smooth Muscle	Colon
8	chr5:58626200-58629400	Weak transcription	Hela-S3	cervix
9	chr5:58626600-58629200	Genic enhancers	A549	lung
10	chr5:58626800-58631000	Weak transcription	Psoas Muscle	Psoas
11	chr5:58627200-58630000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:58627200-58634400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr5:58627400-58641600	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr5:58628200-58629400	Enhancers	Fetal Heart	heart
15	chr5:58628400-58629600	Enhancers	Fetal Lung	lung
16	chr5:58628600-58628800	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:58628600-58628800	Enhancers	Gastric	stomach
18	chr5:58628600-58628800	Enhancers	Right Atrium	heart
19	chr5:58628600-58629000	Enhancers	HUES48 Cell Line	embryonic stem cell

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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