Variant report

Variant	rs1350415
Chromosome Location	chr3:55913237-55913238
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1350414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1458067	0.91[AFR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1458068	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1993539	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4955877	0.94[CHB][hapmap]
rs4955878	0.94[CHB][hapmap]
rs72879133	0.81[AFR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7432905	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9815001	0.82[CHB][hapmap]
rs9818424	0.83[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9835091	0.85[CHB][hapmap]
rs9852746	0.82[CHB][hapmap]
rs9852888	0.82[CHB][hapmap]
rs9853067	0.86[CHB][hapmap]
rs9857973	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9881976	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	nsv1013063	chr3:55835413-56173713	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv876815	chr3:55895409-55979964	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1350415	ERC2	cis	cerebellum	SCAN
rs1350415	HESX1	cis	cerebellum	SCAN
rs1350415	IQCF1	cis	cerebellum	SCAN
rs1350415	OR7G2	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:55893600-55923600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:55903800-55922000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:55909200-55913400	Weak transcription	A549	lung
4	chr3:55912200-55916000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr3:55912400-55913400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:55912800-55914600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr3:55913000-55913400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr3:55913000-55914000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr3:55913200-55913400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr3:55913200-55913400	Enhancers	Fetal Kidney	kidney
11	chr3:55913200-55914000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr3:55913200-55914600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr3:55913200-55914800	Enhancers	Fetal Lung	lung
14	chr3:55913200-55916800	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr3:55913200-55916800	Enhancers	iPS-20b 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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