Variant report

Variant	rs7990054
Chromosome Location	chr13:96134600-96134601
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10219866	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11617639	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11619150	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11843974	0.87[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs12427460	0.87[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs12866697	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12872431	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12876693	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12876913	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1570903	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1570904	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1890373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4322517	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4335657	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4351928	0.89[ASN][1000 genomes]
rs4387474	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4394950	0.87[CHB][hapmap];0.84[JPT][hapmap];0.84[YRI][hapmap];0.91[ASN][1000 genomes]
rs4402421	0.83[ASN][1000 genomes]
rs4403921	0.86[ASN][1000 genomes]
rs4408415	0.86[ASN][1000 genomes]
rs4409957	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4466958	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4547209	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4564445	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4564446	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4587819	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4609701	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4771917	0.86[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs4773907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773908	0.87[CHB][hapmap];0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs4773909	0.90[ASN][1000 genomes]
rs4773910	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4773911	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4773912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492792	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492793	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6492796	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492797	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492798	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492799	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6492807	0.82[CHB][hapmap];0.93[CHD][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7139829	0.91[ASN][1000 genomes]
rs7322391	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326265	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326546	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7328468	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332888	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332917	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7338647	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7489425	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7982486	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7982563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7984234	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7992297	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7995104	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7995114	0.83[ASN][1000 genomes]
rs7995959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002444	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8002639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877960	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs877961	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs877962	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs927786	0.87[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs927787	0.87[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs927788	0.82[CHB][hapmap];0.91[CHD][hapmap];0.90[ASN][1000 genomes]
rs9302074	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9302075	0.87[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs9302076	0.87[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs946228	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs946231	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516589	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9516590	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516592	0.81[EUR][1000 genomes]
rs9524982	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524983	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524984	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524986	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524987	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9524988	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9524989	0.87[CHB][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs9524991	0.82[CHB][hapmap];0.88[CHD][hapmap];0.87[ASN][1000 genomes]
rs9561880	0.96[ASN][1000 genomes]
rs9590285	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9590286	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9590287	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9590288	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043019	chr13:95924585-96152616	Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1037673	chr13:95930191-96146554	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv541882	chr13:95930191-96146554	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv2752652	chr13:96059024-96181597	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7990054	MBNL2	cis	cerebellum	SCAN
rs7990054	FARP1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96127800-96144600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:96131200-96134600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr13:96131200-96137200	Weak transcription	Aorta	Aorta
4	chr13:96131200-96137200	Weak transcription	Right Atrium	heart
5	chr13:96133000-96136400	Weak transcription	K562	blood
6	chr13:96133600-96137200	Weak transcription	Spleen	Spleen
7	chr13:96133600-96137400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr13:96133800-96135800	Weak transcription	Pancreas	Pancrea
9	chr13:96133800-96137200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:96133800-96137200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr13:96133800-96137200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr13:96133800-96137200	Weak transcription	HUVEC	blood vessel
13	chr13:96134000-96137200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr13:96134000-96137200	Weak transcription	HMEC	breast
15	chr13:96134000-96137400	Weak transcription	Osteobl	bone
16	chr13:96134200-96135800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr13:96134200-96137200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:96134200-96137400	Weak transcription	Primary hematopoietic stem cells	blood
19	chr13:96134400-96136000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr13:96134400-96137400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr13:96134600-96134800	Enhancers	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links