Variant report

Variant	rs12898460
Chromosome Location	chr15:38986813-38986814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:38982044..38984974-chr15:38985840..38987447,2	MCF-7	breast:
2	chr15:38855702..38858314-chr15:38985984..38988881,2	MCF-7	breast:

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

Variant related genes	Relation type
ENSG00000172575	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12148859	0.83[ASN][1000 genomes]
rs12899449	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12901215	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12903120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12912251	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]
rs12916379	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2132157	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2172835	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34141940	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34281605	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34356257	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35024396	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35102843	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35795311	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36094159	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71403553	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7163869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7165988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7177621	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7183893	0.89[AMR][1000 genomes];0.92[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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12898460	FLJ35695	cis	multi-tissue	Pritchard

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	chr15:38983400-38987000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr15:38983800-38987200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr15:38984400-38987200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr15:38984400-38988200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr15:38984600-38988200	Weak transcription	Primary T cells from cord blood	blood
12	chr15:38984800-38987800	Weak transcription	Fetal Thymus	thymus
13	chr15:38984800-38988000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr15:38984800-38988000	Weak transcription	Placenta	Placenta
15	chr15:38984800-38988200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:38984800-38988400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:38985000-38987200	Weak transcription	GM12878-XiMat	blood
18	chr15:38985400-38988200	Weak transcription	Left Ventricle	heart
19	chr15:38985800-38988400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr15:38986200-38988400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr15:38986200-38988800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr15:38986600-38992600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr15:38986600-38992600	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr15:38986800-38989200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr15:38986800-38992400	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr15:38986800-38992600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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