Variant report

Variant	rs1148408
Chromosome Location	chr12:106665078-106665079
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:106640852..106642497-chr12:106662521..106665249,2	MCF-7	breast:
2	chr12:106664388..106667969-chr12:106668032..106670678,3	MCF-7	breast:
3	chr12:106664569..106666975-chr12:106671513..106673721,2	MCF-7	breast:
4	chr12:106639675..106642862-chr12:106661081..106665256,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136026	Chromatin interaction
ENSG00000258355	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10507210	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10746057	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10778460	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10861566	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs10861567	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10861569	0.88[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11112924	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11112926	0.83[ASN][1000 genomes]
rs11112927	0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11112928	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1148409	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1148410	0.95[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1148411	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1148412	0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.97[ASN][1000 genomes]
rs1148442	0.95[ASN][1000 genomes]
rs1148443	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1215808	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230190	0.95[ASN][1000 genomes]
rs12823006	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2047545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279760	0.81[JPT][hapmap]
rs7304941	0.81[JPT][hapmap]
rs7308143	0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7311121	0.96[ASN][1000 genomes]
rs7311133	0.96[ASN][1000 genomes]
rs7315560	0.96[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1148408	CCDC53	cis	cerebellum	SCAN
rs1148408	ISCU	cis	cerebellum	SCAN
rs1148408	GLT8D2	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:106661600-106669000	Weak transcription	Psoas Muscle	Psoas
2	chr12:106662000-106665200	Weak transcription	Fetal Heart	heart
3	chr12:106663400-106666800	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr12:106663600-106665400	Enhancers	Primary neutrophils fromperipheralblood	blood
5	chr12:106664000-106668200	Weak transcription	Spleen	Spleen
6	chr12:106664400-106666800	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr12:106664600-106666200	Enhancers	Pancreas	Pancrea
8	chr12:106664800-106665200	Enhancers	Skeletal Muscle Female	skeletal muscle
9	chr12:106664800-106665800	Enhancers	Skeletal Muscle Male	skeletal muscle
10	chr12:106664800-106666400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr12:106664800-106666600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr12:106664800-106669600	Enhancers	Stomach Mucosa	stomach
13	chr12:106665000-106665600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:106665000-106666200	Enhancers	Liver	Liver
15	chr12:106665000-106668400	Weak transcription	Esophagus	oesophagus

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