Variant report

Variant	rs12912251
Chromosome Location	chr15:38986368-38986369
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	WRNIP1	chr15:38986180-38986501	GM12878	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:38985952..38986472-chr15:56138356..56138929,2	K562	blood:
2	chr15:38982044..38984974-chr15:38985840..38987447,2	MCF-7	breast:
3	chr15:38855702..38858314-chr15:38985984..38988881,2	MCF-7	breast:
4	chr15:38985951..38986452-chr15:56138061..56138588,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C15orf53-2	chr15:38986243-38987176	l_1145_chr15:38986242-38988846_testes

No data

Variant related genes	Relation type
C15orf53	TF binding region
ENSG00000172575	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12148859	0.83[ASN][1000 genomes]
rs12898460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899449	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12901215	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12903120	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12916379	1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2132157	1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2172835	1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34141940	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34281605	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34356257	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35024396	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35102843	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35795311	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs36094159	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71403553	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7165988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177621	0.87[EUR][1000 genomes]
rs7183893	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949171	chr15:38232548-39033746	Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1046994	chr15:38806163-39239014	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv525770	chr15:38816833-39084956	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1054651	chr15:38827825-39082844	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv542358	chr15:38827825-39082844	Bivalent/Poised TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

Variant related diseases (count:2)

Disease	PMID	Source
Bipolar disorder	21926972	GWAS catalog
Bipolar disorder and major depressive disorder (combined)	20351715	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12912251	FLJ35695	cis	multi-tissue	Pritchard
rs12912251	C15orf54	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38976800-38987200	Weak transcription	Primary hematopoietic stem cells	blood
2	chr15:38978800-38990800	Weak transcription	Right Atrium	heart
3	chr15:38982400-38988000	Weak transcription	Thymus	Thymus
4	chr15:38983000-38987400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:38983200-38987200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr15:38983200-38987200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:38983400-38986600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:38983400-38986800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr15:38983400-38986800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:38983400-38987000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr15:38983800-38986800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:38983800-38987200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:38984400-38987200	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr15:38984400-38988200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr15:38984600-38988200	Weak transcription	Primary T cells from cord blood	blood
16	chr15:38984800-38986600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr15:38984800-38987800	Weak transcription	Fetal Thymus	thymus
18	chr15:38984800-38988000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr15:38984800-38988000	Weak transcription	Placenta	Placenta
20	chr15:38984800-38988200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr15:38984800-38988400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:38985000-38987200	Weak transcription	GM12878-XiMat	blood
23	chr15:38985400-38988200	Weak transcription	Left Ventricle	heart
24	chr15:38985800-38988400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr15:38986200-38988400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:38986200-38988800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood

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