Variant report

Variant	rs12199702
Chromosome Location	chr6:36127469-36127470
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10447375	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10447396	0.96[CEU][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1059227	1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.85[ASN][1000 genomes]
rs10947589	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12193895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12201042	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12201072	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12525283	1.00[JPT][hapmap]
rs17715809	1.00[JPT][hapmap]
rs2007683	0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2859135	0.84[AMR][1000 genomes]
rs2859136	0.88[MEX][hapmap];0.82[AMR][1000 genomes]
rs2859137	0.84[AMR][1000 genomes]
rs2859141	0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6940723	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][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	esv3363467	chr6:35820920-36222197	Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12199702	MAPK13	Cis_1M	lymphoblastoid	RTeQTL
rs12199702	MAPK13	cis	Esophagus Mucosa	GTEx
rs12199702	SRPK1	cis	cerebellum	SCAN
rs12199702	MAPK13	cis	Skin Sun Exposed Lower leg	GTEx
rs12199702	KIF6	cis	cerebellum	SCAN
rs12199702	MAPK13	cis	parietal	SCAN
rs12199702	BAK1	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:36101200-36129400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr6:36110000-36145000	Weak transcription	Primary T cells from cord blood	blood
3	chr6:36110200-36137200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr6:36118000-36127800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:36118000-36129000	Weak transcription	HepG2	liver
6	chr6:36118600-36145800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr6:36122600-36128000	Weak transcription	Ovary	ovary
8	chr6:36124400-36128000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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