Variant report

Variant	rs3807125
Chromosome Location	chr7:128354937-128354938
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10276394	0.82[ASN][1000 genomes]
rs11973846	0.88[TSI][hapmap]
rs339078	0.80[CHD][hapmap];0.84[JPT][hapmap]
rs3807126	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4283986	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4307280	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs4731507	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4731508	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6946321	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72607753	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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	nsv427806	chr7:128179989-128428182	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv1016979	chr7:128333070-128534438	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3807125	KLHDC10	cis	parietal	SCAN
rs3807125	LRRC4	cis	cerebellum	SCAN
rs3807125	OPN1SW	cis	cerebellum	SCAN
rs3807125	TMEM209	cis	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:128339000-128358800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr7:128349400-128378600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr7:128349800-128378200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:128349800-128378400	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:128351200-128355000	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr7:128353400-128355000	Enhancers	HMEC	breast
7	chr7:128353400-128355200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:128353400-128355200	Enhancers	NHEK	skin
9	chr7:128354000-128355600	Enhancers	HUVEC	blood vessel
10	chr7:128354200-128355200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr7:128354600-128355000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:128354600-128355400	Enhancers	Spleen	Spleen
13	chr7:128354600-128355400	Bivalent Enhancer	K562	blood
14	chr7:128354600-128356200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr7:128354800-128355400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr7:128354800-128355600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:128354800-128356000	Enhancers	hESC Derived CD56+ Mesoderm 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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