Variant report

Variant	rs2049963
Chromosome Location	chr1:186851216-186851217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10798065	0.87[ASN][1000 genomes]
rs10798066	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16826042	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16826060	0.90[JPT][hapmap]
rs1980444	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];1.00[ASN][1000 genomes]
rs2064115	0.82[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2205898	0.94[ASN][1000 genomes]
rs2223309	0.90[JPT][hapmap];0.86[MEX][hapmap]
rs7540602	0.86[CHD][hapmap];0.95[JPT][hapmap];0.86[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	nsv872590	chr1:186557453-187500338	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv947343	chr1:186846236-186851365	Enhancers Weak transcription Strong transcription	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2049963	GLT25D2	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:186839200-186884800	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:186841000-186853600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:186841000-186853800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:186841800-186862400	Weak transcription	Hela-S3	cervix
5	chr1:186843400-186853800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:186844200-186851600	Weak transcription	HUES64 Cell Line	embryonic stem cell
7	chr1:186845200-186851400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:186845200-186856800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:186846600-186851600	Weak transcription	NHDF-Ad	bronchial
10	chr1:186848000-186856000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr1:186848400-186852600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:186848600-186851600	Enhancers	Colon Smooth Muscle	Colon
13	chr1:186849200-186852000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:186850600-186856400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:186850800-186853800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:186850800-186862200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr1:186850800-186863400	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:186850800-186865400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr1:186851000-186851400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr1:186851200-186852000	Enhancers	Placenta Amnion	Placenta Amnion
21	chr1:186851200-186852400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:186851200-186856000	Weak transcription	Rectal Smooth Muscle	rectum

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