Variant report

Variant	rs6485644
Chromosome Location	chr11:45855998-45855999
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45854327..45856053-chr11:45869325..45871424,2	K562	blood:
2	chr11:45845665..45849726-chr11:45853081..45856050,3	K562	blood:
3	chr11:45824552..45827544-chr11:45855388..45857462,2	MCF-7	breast:
4	chr11:45851162..45853664-chr11:45855593..45858334,2	K562	blood:

Variant related genes	Relation type
ENSG00000181830	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10838524	0.98[GIH][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs11038672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11038673	0.90[CHB][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs11038678	0.98[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11038694	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11605924	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11607182	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11607883	1.00[CEU][hapmap];0.84[CHB][hapmap];0.80[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12419690	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12794698	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12805422	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12807179	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1401419	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34043764	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6485645	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6485646	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7105751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7112505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7115753	0.83[EUR][1000 genomes]
rs7121611	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7933420	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7945565	1.00[ASW][hapmap];0.89[CEU][hapmap];0.98[GIH][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7945689	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897314	chr11:45816020-45965129	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6485644	PEX16	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45845800-45869000	Weak transcription	Right Atrium	heart
2	chr11:45853600-45856000	Weak transcription	Skeletal Muscle Male	skeletal muscle
3	chr11:45854000-45856400	Enhancers	Placenta	Placenta
4	chr11:45854400-45856400	Flanking Active TSS	Dnd41	blood
5	chr11:45854600-45856400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr11:45854800-45856600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr11:45855200-45856000	Enhancers	Hela-S3	cervix
8	chr11:45855200-45856200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr11:45855200-45856400	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr11:45855200-45856400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:45855200-45856400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr11:45855400-45856400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr11:45855400-45856400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr11:45855400-45856400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr11:45855400-45856400	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr11:45855400-45856400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:45855800-45856200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:45855800-45856200	Enhancers	Gastric	stomach
19	chr11:45855800-45856200	Enhancers	Left Ventricle	heart
20	chr11:45855800-45856200	Enhancers	Ovary	ovary
21	chr11:45855800-45856400	Enhancers	Primary T cells from cord blood	blood
22	chr11:45855800-45856400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
23	chr11:45855800-45856400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr11:45855800-45856400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr11:45855800-45856400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr11:45855800-45856400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr11:45855800-45856400	Enhancers	Adipose Nuclei	Adipose
28	chr11:45855800-45856400	Enhancers	Liver	Liver
29	chr11:45855800-45856400	Flanking Active TSS	K562	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links