Variant report

Variant	rs4813133
Chromosome Location	chr20:1403686-1403687
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:1396677..1398342-chr20:1402611..1404331,2	MCF-7	breast:
2	chr20:1402742..1405514-chr20:1452729..1455276,2	K562	blood:
3	chr20:1397101..1400734-chr20:1402092..1406050,4	K562	blood:
4	chr20:1397917..1400734-chr20:1402889..1405956,3	K562	blood:

Variant related genes	Relation type
ENSG00000088833	Chromatin interaction

Extended variants
information (count: 84 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11087052	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs1884389	0.85[CHB][hapmap];0.82[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1998007	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2144542	0.93[ASN][1000 genomes]
rs2144543	0.93[ASN][1000 genomes]
rs2144545	0.84[JPT][hapmap]
rs2207828	0.84[ASN][1000 genomes]
rs2207829	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2207830	0.96[ASN][1000 genomes]
rs3088080	0.84[JPT][hapmap]
rs36018423	0.93[ASN][1000 genomes]
rs3829698	0.86[CHD][hapmap];0.88[JPT][hapmap]
rs4814229	0.85[ASN][1000 genomes]
rs4814231	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4814237	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs4814240	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs4814243	0.85[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.95[ASN][1000 genomes]
rs4814244	0.92[CHB][hapmap];0.89[ASN][1000 genomes]
rs5019244	0.93[ASN][1000 genomes]
rs6033691	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6033697	0.85[ASN][1000 genomes]
rs6033698	0.85[ASN][1000 genomes]
rs6033707	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6033709	0.85[ASN][1000 genomes]
rs6033710	0.93[CHB][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs6033715	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs6033726	0.93[ASN][1000 genomes]
rs6033728	0.93[ASN][1000 genomes]
rs6033729	0.93[ASN][1000 genomes]
rs6033732	0.93[ASN][1000 genomes]
rs6033744	0.93[ASN][1000 genomes]
rs6033753	0.96[ASN][1000 genomes]
rs6033807	0.84[JPT][hapmap]
rs6042066	0.85[ASN][1000 genomes]
rs6042071	0.85[ASN][1000 genomes]
rs6042072	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6042074	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6042088	0.85[ASN][1000 genomes]
rs6042091	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6042117	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs6042118	1.00[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs6042131	0.93[ASN][1000 genomes]
rs6042160	0.93[ASN][1000 genomes]
rs6042170	0.93[ASN][1000 genomes]
rs6042172	0.93[ASN][1000 genomes]
rs6042175	0.93[ASN][1000 genomes]
rs6042197	0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs6042207	0.93[ASN][1000 genomes]
rs6042208	0.93[ASN][1000 genomes]
rs6042209	0.91[ASN][1000 genomes]
rs6042270	0.84[JPT][hapmap]
rs6074593	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6074623	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6079009	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079010	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079012	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079013	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079015	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6079133	0.83[JPT][hapmap]
rs6105079	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6105081	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6105102	1.00[CHB][hapmap];0.84[JPT][hapmap];0.93[ASN][1000 genomes]
rs6105110	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105165	0.84[JPT][hapmap]
rs6109825	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6109893	0.93[ASN][1000 genomes]
rs6109894	0.93[ASN][1000 genomes]
rs6109912	0.93[ASN][1000 genomes]
rs6131468	0.85[ASN][1000 genomes]
rs6134916	0.93[ASN][1000 genomes]
rs6514382	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6514383	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6891	0.84[JPT][hapmap]
rs750424	0.93[ASN][1000 genomes]
rs8124053	0.93[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.85[ASN][1000 genomes]
rs873523	0.91[ASN][1000 genomes]
rs910619	0.84[JPT][hapmap]
rs926977	0.96[ASN][1000 genomes]
rs932524	0.84[JPT][hapmap]
rs9575	0.84[JPT][hapmap]

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	nsv522008	chr20:1340390-1638578	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv432095	chr20:1382500-1420340	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv585206	chr20:1386473-1714362	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv1850632	chr20:1393861-1465597	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4813133	PANK2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:1399800-1404400	Weak transcription	NHLF	lung
2	chr20:1399800-1415000	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr20:1400000-1404200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr20:1400000-1408200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr20:1400000-1410600	Weak transcription	Osteobl	bone
6	chr20:1401800-1404400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr20:1401800-1404600	Enhancers	Placenta	Placenta
8	chr20:1402800-1405600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr20:1403200-1403800	Enhancers	Placenta Amnion	Placenta Amnion
10	chr20:1403200-1404600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr20:1403200-1404800	Enhancers	Primary T cells from cord blood	blood
12	chr20:1403200-1405600	Enhancers	HMEC	breast
13	chr20:1403200-1406000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr20:1403200-1406200	Enhancers	NHEK	skin
15	chr20:1403200-1408000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr20:1403400-1404400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
17	chr20:1403600-1403800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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