Variant report

Variant	rs12366826
Chromosome Location	chr12:4916299-4916300
allele	C/T
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	NFYB	chr12:4916292-4916625	GM12878	blood:	n/a	n/a
2	PAX5	chr12:4916190-4916571	GM12878	blood:	n/a	n/a
3	BATF	chr12:4916281-4916557	GM12878	blood:	n/a	n/a
4	BATF	chr12:4915890-4916607	GM12878	blood:	n/a	n/a
5	IKZF1	chr12:4916233-4917309	GM12878	blood:	n/a	n/a
6	BHLHE40	chr12:4915904-4916563	GM12878	blood:	n/a	n/a
7	EP300	chr12:4916234-4916670	GM12878	blood:	n/a	chr12:4916361-4916375
8	RUNX3	chr12:4916229-4917462	GM12878	blood:	n/a	chr12:4916503-4916512 chr12:4916503-4916512
9	NFIC	chr12:4915808-4916700	GM12878	blood:	n/a	n/a
10	EP300	chr12:4916205-4917475	GM12878	blood:	n/a	chr12:4917201-4917208 chr12:4916361-4916375
11	NFIC	chr12:4915979-4916775	GM12878	blood:	n/a	n/a
12	RUNX3	chr12:4915920-4917486	GM12878	blood:	n/a	chr12:4916503-4916512 chr12:4916503-4916512
13	TCF12	chr12:4916248-4916523	GM12878	blood:	n/a	chr12:4916392-4916402

Variant related genes	Relation type
KCNA6	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10849145	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.90[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849146	0.85[ASN][1000 genomes]
rs10849147	0.85[ASN][1000 genomes]
rs10849149	0.85[ASN][1000 genomes]
rs10849153	1.00[JPT][hapmap]
rs11063351	0.85[ASN][1000 genomes]
rs61907137	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61907139	0.85[ASN][1000 genomes]
rs61907144	0.85[ASN][1000 genomes]
rs6489576	1.00[JPT][hapmap]
rs7296238	0.85[ASN][1000 genomes]
rs7297694	0.85[ASN][1000 genomes]
rs7311419	0.85[ASN][1000 genomes]
rs7963542	0.85[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12366826	TSPAN9	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4884400-4918200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr12:4901000-4917800	Weak transcription	Brain Germinal Matrix	brain
3	chr12:4901200-4917800	Weak transcription	Fetal Brain Female	brain
4	chr12:4903800-4917600	Weak transcription	Fetal Brain Male	brain
5	chr12:4915400-4918000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:4915400-4918200	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr12:4915600-4916400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr12:4915600-4916800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:4915600-4917600	Enhancers	GM12878-XiMat	blood
10	chr12:4915600-4917800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr12:4915600-4918000	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr12:4915600-4920000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr12:4915800-4916800	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr12:4915800-4917800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr12:4915800-4918000	Enhancers	Dnd41	blood
16	chr12:4915800-4918600	Enhancers	Primary T cells from cord blood	blood
17	chr12:4916000-4917200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr12:4916000-4917400	Enhancers	Primary T cells fromperipheralblood	blood
19	chr12:4916200-4916400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:4916200-4916400	Enhancers	Fetal Thymus	thymus
21	chr12:4916200-4917400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:4916200-4917400	Bivalent Enhancer	Thymus	Thymus
23	chr12:4916200-4917600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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