Variant report

Variant	rs1874252
Chromosome Location	chr15:38962756-38962757
allele	A/C
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	EP300	chr15:38962682-38963321	GM12878	blood:	n/a	chr15:38962888-38962901
2	EP300	chr15:38962452-38963423	GM12878	blood:	n/a	chr15:38962888-38962901
3	CREB1	chr15:38962605-38963424	GM12878	blood:	n/a	n/a
4	NFYB	chr15:38962702-38963604	GM12878	blood:	n/a	n/a
5	MTA3	chr15:38962710-38963580	GM12878	blood:	n/a	n/a
6	YY1	chr15:38962688-38962987	GM12891	blood:	n/a	n/a
7	YY1	chr15:38962642-38962975	GM12892	blood:	n/a	n/a
8	NFIC	chr15:38962629-38963421	GM12878	blood:	n/a	n/a
9	YY1	chr15:38962624-38962980	GM12892	blood:	n/a	n/a
10	FOXM1	chr15:38962711-38963328	GM12878	blood:	n/a	n/a
11	CUX1	chr15:38962411-38964333	GM12878	blood:	n/a	n/a
12	YY1	chr15:38962622-38963027	GM12878	blood:	n/a	n/a
13	WRNIP1	chr15:38962498-38963283	GM12878	blood:	n/a	n/a
14	EP300	chr15:38962344-38964441	GM12878	blood:	n/a	chr15:38963830-38963840 chr15:38963628-38963637 chr15:38962888-38962901 chr15:38963614-38963628
15	CREB1	chr15:38962269-38963562	GM12878	blood:	n/a	n/a
16	RUNX3	chr15:38962250-38963485	GM12878	blood:	n/a	n/a
17	PML	chr15:38962697-38964505	GM12878	blood:	n/a	n/a
18	RUNX3	chr15:38962756-38963373	GM12878	blood:	n/a	n/a
19	ATF2	chr15:38962714-38963310	GM12878	blood:	n/a	n/a
20	EBF1	chr15:38962315-38963338	GM12878	blood:	n/a	n/a
21	POLR2A	chr15:38962302-38965951	Raji	blood:	n/a	n/a
22	RCOR1	chr15:38962454-38964561	GM12878	blood:	n/a	n/a
23	MTA3	chr15:38962678-38963390	GM12878	blood:	n/a	n/a
24	RELA	chr15:38962660-38963330	GM19099	blood:	n/a	n/a
25	TBL1XR1	chr15:38962279-38964460	GM12878	blood:	n/a	n/a
26	BHLHE40	chr15:38962379-38964425	GM12878	blood:	n/a	n/a
27	TBP	chr15:38962246-38965662	GM12878	blood:	n/a	n/a
28	YY1	chr15:38962682-38962991	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:38855739..38857440-chr15:38962653..38964526,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259747	TF binding region
ENSG00000172575	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs4924287	0.88[CHD][hapmap]
rs6495988	0.93[ASN][1000 genomes]
rs7165355	0.95[ASN][1000 genomes]
rs7168475	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv904085	chr15:38786114-38985513	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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:1)

Disease	PMID	Source
Alcohol dependence (age at onset)	24962325	GWAS catalog

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:38949600-38963800	Enhancers	Primary T cells from cord blood	blood
2	chr15:38955200-38963200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr15:38955200-38963600	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr15:38956000-38964000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr15:38956000-38964800	Enhancers	Primary T killer memory cells from peripheral blood	blood
6	chr15:38956200-38967600	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr15:38956800-38964000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr15:38957000-38964200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr15:38959000-38967400	Enhancers	Primary T cells fromperipheralblood	blood
10	chr15:38959400-38964800	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr15:38959800-38963600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:38960000-38964200	Weak transcription	Spleen	Spleen
13	chr15:38960800-38963400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:38960800-38964000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr15:38961000-38964400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr15:38961200-38964000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:38961400-38963800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:38961600-38964200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:38961800-38963000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr15:38961800-38964000	Enhancers	Fetal Thymus	thymus
21	chr15:38961800-38965800	Enhancers	Thymus	Thymus
22	chr15:38962000-38962800	Enhancers	GM12878-XiMat	blood
23	chr15:38962000-38963800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr15:38962000-38964000	Enhancers	Dnd41	blood
25	chr15:38962000-38966600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:38962000-38967000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:38962000-38967200	Enhancers	Primary B cells from peripheral blood	blood
28	chr15:38962200-38962800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:38962200-38968600	Enhancers	Primary B cells from cord blood	blood
30	chr15:38962400-38962800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr15:38962400-38963000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
32	chr15:38962600-38962800	Enhancers	Rectal Mucosa Donor 29	rectum
33	chr15:38962600-38964200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr15:38962600-38965600	Enhancers	Primary hematopoietic stem cells	blood

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