Variant report

Variant	rs11068006
Chromosome Location	chr12:116803557-116803558
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	IRF1	chr12:116803225-116803648	K562	blood:	n/a	n/a
2	GATA3	chr12:116802839-116803900	A549	lung:	n/a	n/a
3	CEBPB	chr12:116803444-116803717	K562	blood:	n/a	n/a
4	EP300	chr12:116802803-116804177	A549	lung:	n/a	chr12:116803419-116803433

No.	Distal block	Cell Line	Cell type
1	chr12:116715387..116717811-chr12:116800795..116804435,3	MCF-7	breast:
2	chr12:116716333..116718109-chr12:116803555..116806068,2	K562	blood:
3	chr12:116713535..116717387-chr12:116803104..116806082,3	MCF-7	breast:
4	chr12:116796063..116798440-chr12:116800677..116803897,4	K562	blood:

Variant related genes	Relation type
ENSG00000258346	TF binding region
ENSG00000123066	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10850618	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10850619	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11068003	1.00[ASW][hapmap];0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11068007	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12228903	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs12230486	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs12371905	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17615178	1.00[LWK][hapmap]
rs57615867	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11068006	SLC24A6	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:116796800-116803800	Weak transcription	Colonic Mucosa	Colon
2	chr12:116797400-116803800	Weak transcription	Pancreas	Pancrea
3	chr12:116797600-116807800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr12:116797800-116806200	Weak transcription	Liver	Liver
5	chr12:116798000-116807800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr12:116799000-116803800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr12:116799200-116803800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:116799400-116814800	Weak transcription	Spleen	Spleen
9	chr12:116799600-116804000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr12:116799600-116804000	Weak transcription	Lung	lung
11	chr12:116799600-116804200	Weak transcription	Psoas Muscle	Psoas
12	chr12:116799600-116806000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr12:116799800-116804000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr12:116799800-116806200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:116800000-116803800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:116800000-116804200	Weak transcription	Fetal Muscle Leg	muscle
17	chr12:116800800-116804000	Weak transcription	Dnd41	blood
18	chr12:116800800-116820600	Weak transcription	Thymus	Thymus
19	chr12:116801400-116804400	Weak transcription	Fetal Thymus	thymus
20	chr12:116802200-116812000	Enhancers	Placenta	Placenta
21	chr12:116802400-116804000	Enhancers	GM12878-XiMat	blood
22	chr12:116802400-116804400	Enhancers	Hela-S3	cervix
23	chr12:116802400-116804400	Enhancers	K562	blood
24	chr12:116803000-116804400	Enhancers	HUVEC	blood vessel
25	chr12:116803000-116805000	Enhancers	Duodenum Mucosa	Duodenum
26	chr12:116803000-116805200	Enhancers	Small Intestine	intestine
27	chr12:116803400-116803600	Flanking Active TSS	A549	lung
28	chr12:116803400-116804000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:116803400-116804200	Enhancers	Fetal Intestine Large	intestine
30	chr12:116803400-116805200	Enhancers	Stomach Mucosa	stomach

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