Variant report

Variant	rs7163869
Chromosome Location	chr15:38988391-38988392
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RUNX3	chr15:38988172-38989078	GM12878	blood:	n/a	n/a
2	EP300	chr15:38988112-38988553	SK-N-SH_RA	brain:	n/a	n/a
3	POLR2A	chr15:38988105-38988887	GM12892	blood:	n/a	n/a
4	POLR2A	chr15:38988116-38989136	GM18951	blood:	n/a	n/a
5	POLR2A	chr15:38987602-38989220	GM19193	blood:	n/a	n/a
6	MYC	chr15:38988390-38988468	GM12878	blood:	n/a	n/a
7	GATA2	chr15:38987204-38988519	SH-SY5Y	brain:	n/a	n/a
8	POLR2A	chr15:38988234-38988859	GM12892	blood:	n/a	n/a
9	POLR2A	chr15:38988337-38988750	GM12892	blood:	n/a	n/a
10	EP300	chr15:38987805-38988478	SK-N-SH_RA	brain:	n/a	n/a
11	MYC	chr15:38988162-38989068	NB4	blood:	n/a	n/a
12	TCF12	chr15:38987459-38988532	SK-N-SH	brain:	n/a	chr15:38988146-38988153
13	POLR2A	chr15:38988363-38988907	GM12892	blood:	n/a	n/a
14	RELA	chr15:38987610-38989052	GM19193	blood:	n/a	n/a
15	MAX	chr15:38988389-38989119	NB4	blood:	n/a	n/a

No data

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

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

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C15orf53-2	chr15:38988296-38989826	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: 1 )

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

rs_ID	r²[population]
rs12148859	0.81[ASN][1000 genomes]
rs12898460	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]
rs12899449	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12901215	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12903120	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12912251	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]
rs12916379	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2132157	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2172835	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34141940	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34281605	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs34356257	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35024396	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35102843	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35795311	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36094159	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs71403553	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7165988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7171233	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7177621	0.89[EUR][1000 genomes]
rs7183893	0.90[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
rs7163869	FLJ35695	cis	multi-tissue	Pritchard

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38978800-38990800	Weak transcription	Right Atrium	heart
2	chr15:38984800-38988400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr15:38985800-38988400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
4	chr15:38986200-38988400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
5	chr15:38986200-38988800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:38986600-38992600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr15:38986600-38992600	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr15:38986800-38989200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr15:38986800-38992400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr15:38986800-38992600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr15:38987000-38992000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr15:38987200-38988800	Enhancers	Primary T cells fromperipheralblood	blood
13	chr15:38987200-38989200	Enhancers	GM12878-XiMat	blood
14	chr15:38987200-38989400	Enhancers	Fetal Heart	heart
15	chr15:38987200-38991800	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr15:38987200-38992000	Enhancers	Primary hematopoietic stem cells	blood
17	chr15:38987200-38992400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr15:38987200-38992600	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr15:38987600-38988800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
20	chr15:38987800-38991400	Enhancers	Dnd41	blood
21	chr15:38987800-38991800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr15:38987800-38991800	Enhancers	Fetal Thymus	thymus
23	chr15:38988000-38988800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:38988000-38989000	Enhancers	Placenta	Placenta
25	chr15:38988000-38989000	Enhancers	Thymus	Thymus
26	chr15:38988000-38989400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:38988000-38989400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:38988200-38988600	Enhancers	Rectal Mucosa Donor 31	rectum
29	chr15:38988200-38988600	Enhancers	Spleen	Spleen
30	chr15:38988200-38989000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr15:38988200-38989000	Enhancers	Left Ventricle	heart
32	chr15:38988200-38989000	Enhancers	Sigmoid Colon	Sigmoid Colon
33	chr15:38988200-38989000	Enhancers	HSMM	muscle
34	chr15:38988200-38989000	Enhancers	NH-A	brain
35	chr15:38988200-38989400	Enhancers	Primary T cells from cord blood	blood
36	chr15:38988200-38989400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr15:38988200-38990200	Enhancers	Duodenum Mucosa	Duodenum

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