Variant report

Variant	rs4129472
Chromosome Location	chr5:42523172-42523173
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10041108	1.00[CHB][hapmap]
rs10440649	1.00[CHB][hapmap]
rs11957404	1.00[CHB][hapmap]
rs13156541	1.00[CHB][hapmap]
rs13168764	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13171720	1.00[CHB][hapmap]
rs13182117	1.00[CHB][hapmap]
rs13184352	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13188386	1.00[CHB][hapmap]
rs13354167	1.00[CHB][hapmap]
rs17574527	1.00[CHB][hapmap]
rs17574616	1.00[CHB][hapmap]
rs17575164	1.00[CHB][hapmap]
rs17636762	1.00[CHB][hapmap]
rs28943880	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28943882	1.00[CHB][hapmap]
rs33939197	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34975809	1.00[ASN][1000 genomes]
rs35003055	1.00[ASN][1000 genomes]
rs35185573	1.00[ASN][1000 genomes]
rs35525634	1.00[ASN][1000 genomes]
rs35920615	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4129645	1.00[ASN][1000 genomes]
rs4292454	1.00[CHB][hapmap]
rs5025611	1.00[CHB][hapmap]
rs56144821	1.00[ASN][1000 genomes]
rs6414898	1.00[CHB][hapmap]
rs6451634	1.00[CHB][hapmap]
rs6451641	1.00[CHB][hapmap]
rs67005744	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67277863	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67812331	1.00[ASN][1000 genomes]
rs6863381	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6873340	1.00[CHB][hapmap]
rs6883523	1.00[MEX][hapmap]
rs7444761	1.00[CHB][hapmap]
rs7702524	1.00[CHB][hapmap]
rs7703669	1.00[CHB][hapmap]
rs7709790	1.00[CHB][hapmap]
rs7718962	1.00[CHB][hapmap]
rs9292854	1.00[CHB][hapmap]
rs9763260	1.00[ASN][1000 genomes]

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	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4129472	C6	cis	parietal	SCAN
rs4129472	GYS2	trans	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42516400-42525000	Enhancers	Adipose Nuclei	Adipose
2	chr5:42520200-42523800	Enhancers	Breast Myoepithelial Primary Cells	Breast
3	chr5:42521000-42524800	Weak transcription	Fetal Stomach	stomach
4	chr5:42521400-42523600	Weak transcription	Right Atrium	heart
5	chr5:42521400-42525000	Weak transcription	Psoas Muscle	Psoas
6	chr5:42521600-42523200	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr5:42521600-42526000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr5:42522000-42523800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr5:42522200-42527600	Weak transcription	Fetal Lung	lung
10	chr5:42522400-42523400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr5:42522400-42523800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr5:42522400-42524200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:42522400-42532000	Weak transcription	Liver	Liver
14	chr5:42523000-42523200	Enhancers	Colon Smooth Muscle	Colon
15	chr5:42523000-42523400	Enhancers	NHDF-Ad	bronchial

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Input of quick search could be:

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

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