Variant report

Variant	rs38513
Chromosome Location	chr7:28028227-28028228
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10951189	0.84[CHD][hapmap]
rs12216542	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12671522	0.83[CHB][hapmap];0.85[CHD][hapmap]
rs12671866	0.94[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17156137	1.00[YRI][hapmap]
rs192254	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2107821	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2107822	0.87[EUR][1000 genomes]
rs253310	0.94[CEU][hapmap];0.91[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs38500	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs38502	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs38504	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38507	0.92[AFR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs38511	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs38514	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs38515	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs38516	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs38517	1.00[ASW][hapmap];0.89[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4308621	0.80[ASN][1000 genomes]
rs4357200	0.81[ASN][1000 genomes]
rs4492256	0.81[ASN][1000 genomes]
rs6969285	0.85[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.82[EUR][1000 genomes]
rs72598569	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72598573	0.88[AMR][1000 genomes];0.86[EUR][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	nsv949025	chr7:27578167-28075172	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
2	nsv1030685	chr7:27844038-28177301	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs38513	CYCS	cis	cerebellum	SCAN
rs38513	EVX1	cis	cerebellum	SCAN
rs38513	HOXA13	cis	parietal	SCAN
rs38513	TRIL	cis	parietal	SCAN
rs38513	TRIL	cis	cerebellum	SCAN
rs38513	CPVL	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:28002800-28034600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:28006400-28031800	Weak transcription	NHDF-Ad	bronchial
3	chr7:28013400-28034200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr7:28015600-28032400	Weak transcription	Ovary	ovary
5	chr7:28017600-28042400	Weak transcription	Aorta	Aorta
6	chr7:28020000-28032400	Weak transcription	Primary B cells from cord blood	blood
7	chr7:28022400-28031000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr7:28022400-28036200	Weak transcription	Lung	lung
9	chr7:28026400-28032200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr7:28027200-28029800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:28027200-28045800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr7:28027800-28028400	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:28027800-28039400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr7:28028000-28028400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
15	chr7:28028000-28028400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
16	chr7:28028200-28032800	Weak transcription	Fetal Muscle Leg	muscle

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