Variant report

Variant	rs7598832
Chromosome Location	chr2:67853013-67853014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11904407	0.80[AFR][1000 genomes]
rs17033785	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs17033788	0.81[JPT][hapmap]
rs17033929	0.81[ASN][1000 genomes]
rs17033967	0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs17033981	0.82[ASN][1000 genomes]
rs2861699	1.00[ASW][hapmap];0.91[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4591326	0.84[MEX][hapmap]
rs4671191	0.82[ASN][1000 genomes]
rs4671193	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4671814	0.81[ASN][1000 genomes]
rs6546323	1.00[ASW][hapmap];0.95[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6721459	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7579880	0.84[AFR][1000 genomes]
rs7598674	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534389	chr2:67388428-68225338	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7598832	GMCL1	cis	parietal	SCAN
rs7598832	C2orf42	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:67852200-67854400	Enhancers	Muscle Satellite Cultured Cells	--
2	chr2:67852400-67853200	Enhancers	Adipose Nuclei	Adipose
3	chr2:67852400-67853800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr2:67852400-67854200	Enhancers	HMEC	breast
5	chr2:67852400-67854600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:67852400-67854600	Enhancers	NHDF-Ad	bronchial
7	chr2:67852400-67855000	Enhancers	HSMM	muscle
8	chr2:67852600-67853200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr2:67852600-67853600	Enhancers	Osteobl	bone
10	chr2:67852600-67853800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr2:67852800-67853400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr2:67853000-67853200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr2:67853000-67853200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:67853000-67853200	Flanking Active TSS	NH-A	brain
15	chr2:67853000-67853400	Enhancers	Fetal Stomach	stomach
16	chr2:67853000-67853400	Flanking Active TSS	HSMMtube	muscle
17	chr2:67853000-67853800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr2:67853000-67853800	Enhancers	Fetal Muscle Leg	muscle
19	chr2:67853000-67854600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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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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