Variant report

Variant	rs1570904
Chromosome Location	chr13:96150044-96150045
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96148891..96151318-chr13:96153321..96155668,2	K562	blood:

Extended variants
information (count: 89 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10219866	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11617639	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11619150	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11843974	0.82[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs12427460	0.81[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs12866697	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12872431	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12876693	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12876913	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1570903	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1890373	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4322517	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4335657	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4351928	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4387474	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4394950	0.82[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs4402421	0.81[ASN][1000 genomes]
rs4403921	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4408415	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4409957	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4466958	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4547209	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4564445	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4564446	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4587819	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4609701	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4614587	0.83[EUR][1000 genomes]
rs4771917	0.83[JPT][hapmap];0.91[ASN][1000 genomes]
rs4773907	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4773908	0.81[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs4773909	0.91[ASN][1000 genomes]
rs4773910	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773911	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773912	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492792	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492793	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6492796	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492797	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6492798	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6492799	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6492807	0.93[CHD][hapmap];0.82[ASN][1000 genomes]
rs7139829	0.90[ASN][1000 genomes]
rs7322391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7326265	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7326546	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7328468	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7332888	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7332917	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7338647	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7489425	0.85[ASN][1000 genomes]
rs7982486	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7982563	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7984234	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7990054	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]
rs7992297	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7995104	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7995114	0.81[ASN][1000 genomes]
rs7995959	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8002444	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8002639	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs877960	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs877961	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs877962	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs927786	0.82[CHB][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs927787	0.81[CHB][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs927788	0.91[CHD][hapmap];0.91[ASN][1000 genomes]
rs9302074	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9302075	0.81[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs9302076	0.82[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs946228	0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs946231	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9516589	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9516590	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9524982	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524983	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524984	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9524986	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9524987	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524988	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9524989	0.82[CHB][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs9524991	0.88[CHD][hapmap];0.89[ASN][1000 genomes]
rs9561880	0.95[ASN][1000 genomes]
rs9590285	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9590286	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9590287	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9590288	0.84[EUR][1000 genomes];0.94[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	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	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
3	nsv900933	chr13:96138087-96215289	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1570904	UGCGL2	cis	multi-tissue	Pritchard
rs1570904	MBNL2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96145000-96152600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr13:96149000-96150600	Enhancers	Primary hematopoietic stem cells short term culture	blood
3	chr13:96149000-96150600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr13:96149000-96150600	Enhancers	Pancreas	Pancrea
5	chr13:96149000-96152200	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr13:96149200-96150800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr13:96149200-96151800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr13:96149400-96150600	Enhancers	Brain Germinal Matrix	brain
9	chr13:96149600-96150600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr13:96149600-96150800	Enhancers	Fetal Muscle Trunk	muscle
11	chr13:96149600-96150800	Enhancers	Left Ventricle	heart
12	chr13:96149600-96150800	Enhancers	Rectal Smooth Muscle	rectum
13	chr13:96149600-96152800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr13:96149600-96152800	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr13:96149800-96150200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr13:96149800-96150400	Weak transcription	Esophagus	oesophagus
17	chr13:96149800-96150600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr13:96149800-96150600	Enhancers	Fetal Heart	heart
19	chr13:96149800-96150600	Enhancers	Fetal Muscle Leg	muscle
20	chr13:96150000-96150200	Flanking Active TSS	Colon Smooth Muscle	Colon
21	chr13:96150000-96151000	Weak transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links