Variant report

Variant	rs3800624
Chromosome Location	chr7:137375415-137375416
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1019583	0.91[CEU][hapmap];0.85[CHB][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12056089	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[MEX][hapmap]
rs12707364	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12707367	0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs12707372	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1424370	0.91[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.86[ASN][1000 genomes]
rs1424371	0.89[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs1723069	0.80[EUR][1000 genomes]
rs1834143	0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1991084	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2113428	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs270893	0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[EUR][1000 genomes]
rs270894	0.91[CEU][hapmap];0.85[CHB][hapmap];0.90[EUR][1000 genomes]
rs270895	0.91[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs270896	0.91[CEU][hapmap];0.85[CHB][hapmap];0.84[MEX][hapmap];0.90[EUR][1000 genomes]
rs270897	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs270898	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs270899	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs270900	0.87[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs270901	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs270902	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs270904	0.87[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2882781	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3778797	0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3778798	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3800626	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3800628	0.85[ASN][1000 genomes]
rs3800630	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3800637	0.86[CHB][hapmap]
rs4728420	0.95[CEU][hapmap];0.95[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4732263	0.91[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4732264	0.91[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6948537	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6971978	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs6976725	0.95[CEU][hapmap];0.95[CHB][hapmap];0.84[CHD][hapmap];0.87[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7457119	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7806658	0.86[CHB][hapmap];0.82[JPT][hapmap]
rs7806810	0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022793	chr7:137187383-137619359	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv464731	chr7:137356651-137404781	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
3	nsv608466	chr7:137356651-137404781	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3800624	SLC13A4	cis	cerebellum	SCAN
rs3800624	ADCK2	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:137370400-137380600	Weak transcription	Brain Angular Gyrus	brain
2	chr7:137370800-137384600	Weak transcription	Fetal Brain Female	brain
3	chr7:137373400-137380800	Weak transcription	NH-A	brain
4	chr7:137373600-137376000	Weak transcription	HSMM	muscle
5	chr7:137373800-137379200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr7:137374000-137379200	Weak transcription	Osteobl	bone
7	chr7:137374000-137387400	Weak transcription	Aorta	Aorta
8	chr7:137374200-137375800	Genic enhancers	Muscle Satellite Cultured Cells	--
9	chr7:137374400-137378000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr7:137374400-137380600	Weak transcription	HSMMtube	muscle
11	chr7:137374600-137375800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr7:137374800-137375800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr7:137374800-137379200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr7:137374800-137379800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links