Variant report

Variant	rs6545454
Chromosome Location	chr2:55122589-55122590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55120040..55122606-chr2:55452810..55455603,2	K562	blood:
2	chr2:55122046..55124252-chr2:55124464..55126303,3	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10164641	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13383645	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13385982	0.85[ASN][1000 genomes]
rs13408207	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13410462	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1432104	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17346032	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1898699	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6718267	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6729866	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6746577	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72482058	0.91[ASN][1000 genomes]
rs7355309	0.92[CEU][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs7595599	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9309260	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997198	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6545454	CCDC85A	cis	parietal	SCAN
rs6545454	TSPYL6	cis	cerebellum	SCAN
rs6545454	PSME4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55087800-55126000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr2:55095200-55148200	Weak transcription	Primary B cells from peripheral blood	blood
3	chr2:55106600-55124000	Weak transcription	Spleen	Spleen
4	chr2:55107400-55122600	Weak transcription	Brain Substantia Nigra	brain
5	chr2:55109200-55126800	Weak transcription	Brain Angular Gyrus	brain
6	chr2:55109200-55127600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:55119000-55124600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:55119000-55124600	Weak transcription	Fetal Brain Female	brain
9	chr2:55119400-55124600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:55120400-55130200	Weak transcription	Hela-S3	cervix
11	chr2:55122000-55130200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:55122200-55123000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr2:55122400-55122600	ZNF genes & repeats	Fetal Muscle Leg	muscle
14	chr2:55122400-55122800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:55122400-55122800	ZNF genes & repeats	Primary B cells from cord blood	blood
16	chr2:55122400-55123000	ZNF genes & repeats	Brain Anterior Caudate	brain
17	chr2:55122400-55123000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:55122400-55123000	ZNF genes & repeats	HSMMtube	muscle
19	chr2:55122400-55123200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
20	chr2:55122400-55123200	ZNF genes & repeats	HepG2	liver
21	chr2:55122400-55123400	ZNF genes & repeats	Brain Hippocampus Middle	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links