Variant report

Variant	rs8025614
Chromosome Location	chr15:42142912-42142913
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:23)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr15:42142672-42143048	ECC-1	luminal epithelium:	n/a	n/a
2	CEBPB	chr15:42142686-42143065	A549	lung:	n/a	n/a
3	CEBPB	chr15:42142720-42143068	H1-hESC	embryonic stem cell:	n/a	n/a
4	CEBPB	chr15:42142481-42143077	K562	blood:	n/a	n/a
5	POLR2A	chr15:42142516-42142948	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr15:42142214-42143197	K562	blood:	n/a	n/a
7	POLR2A	chr15:42142840-42143047	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr15:42142168-42143640	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr15:42140936-42143751	K562	blood:	n/a	n/a
10	CEBPB	chr15:42142741-42142962	HepG2	liver:	n/a	n/a
11	CEBPB	chr15:42142589-42143068	A549	lung:	n/a	n/a
12	CEBPB	chr15:42142710-42143049	A549	lung:	n/a	n/a
13	CEBPB	chr15:42142786-42142940	K562	blood:	n/a	n/a
14	MTA3	chr15:42142503-42143029	GM12878	blood:	n/a	n/a
15	CEBPB	chr15:42142662-42143131	MCF-7	breast:	n/a	n/a
16	CEBPB	chr15:42142700-42143050	HepG2	liver:	n/a	n/a
17	POLR2A	chr15:42141237-42143747	ECC-1	luminal epithelium:	n/a	n/a
18	CEBPB	chr15:42142668-42143076	MCF-7	breast:	n/a	n/a
19	CEBPB	chr15:42142646-42143071	Hela-S3	cervix:	n/a	n/a
20	CEBPB	chr15:42142652-42143048	K562	blood:	n/a	n/a
21	POLR2A	chr15:42140910-42146784	Hela-S3	cervix:	n/a	n/a
22	CEBPB	chr15:42142620-42143113	ECC-1	luminal epithelium:	n/a	n/a
23	CEBPB	chr15:42142696-42143062	IMR90	lung:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42136531..42140635-chr15:42140718..42144467,4	MCF-7	breast:
2	chr15:42127281..42132563-chr15:42140689..42145219,5	K562	blood:

No data

Variant related genes	Relation type
SPTBN5	TF binding region
ENSG00000168970	Chromatin interaction
ENSG00000243708	Chromatin interaction
ENSG00000243789	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11070349	0.85[CEU][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap]
rs11547012	0.88[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11630242	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11858843	0.84[CEU][hapmap]
rs1197659	0.82[JPT][hapmap]
rs1197668	0.85[CEU][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1197669	0.80[YRI][hapmap]
rs1197672	0.80[YRI][hapmap]
rs1197703	0.96[YRI][hapmap]
rs12439771	0.82[JPT][hapmap]
rs12440605	0.85[CEU][hapmap];0.82[JPT][hapmap];0.91[MEX][hapmap]
rs12591285	0.82[JPT][hapmap]
rs12595271	0.82[JPT][hapmap]
rs12901742	0.82[JPT][hapmap]
rs1918312	0.82[JPT][hapmap]
rs1918313	0.82[JPT][hapmap]
rs2077361	0.82[JPT][hapmap]
rs2077543	0.95[CEU][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2241523	0.88[CEU][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2412640	0.85[CEU][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2577949	0.82[JPT][hapmap]
rs4923907	0.82[JPT][hapmap]
rs4923917	0.89[CEU][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924573	0.82[JPT][hapmap]
rs7166139	0.89[CEU][hapmap];0.82[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7173779	0.82[JPT][hapmap]
rs7174099	0.85[CEU][hapmap];0.82[JPT][hapmap]
rs7175346	0.82[CEU][hapmap];0.81[JPT][hapmap]
rs7177495	0.82[JPT][hapmap]
rs890504	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv904115	chr15:42076387-42171483	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
5	nsv1038393	chr15:42083574-42188035	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
6	esv1827003	chr15:42087505-42199076	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	esv1816120	chr15:42093384-42171578	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
8	nsv1041645	chr15:42095168-42186482	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1051200	chr15:42095168-42188035	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
10	nsv517631	chr15:42096926-42187492	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
11	nsv1051733	chr15:42098896-42186482	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
12	nsv1036153	chr15:42098896-42188035	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
13	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
14	nsv1048606	chr15:42101694-42192760	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
15	nsv904117	chr15:42103822-42184794	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
16	nsv904118	chr15:42103822-42207905	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
17	nsv904119	chr15:42109975-42142912	Genic enhancers Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
18	nsv904120	chr15:42109975-42153085	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
19	nsv904121	chr15:42109975-42162957	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
20	nsv904122	chr15:42109975-42166475	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
21	nsv904123	chr15:42109975-42171483	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
22	nsv904124	chr15:42109975-42207905	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
23	nsv9244	chr15:42110712-42208805	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
24	nsv904125	chr15:42119900-42210393	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
25	nsv1050892	chr15:42128855-42186482	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
26	nsv904126	chr15:42132896-42171483	Enhancers Strong transcription Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
27	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
28	nsv904127	chr15:42142912-42207905	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8025614	RPAP1	cis	parietal	SCAN
rs8025614	NDUFAF1	cis	parietal	SCAN
rs8025614	JMJD7-PLA2G4B	cis	parietal	SCAN
rs8025614	SNAP23	cis	parietal	SCAN
rs8025614	MAPKBP1	cis	cerebellum	SCAN
rs8025614	RPAP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42121000-42147400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:42121400-42147600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:42121400-42147600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:42122200-42145400	Weak transcription	HepG2	liver
5	chr15:42126200-42152400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:42127000-42143600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:42131000-42162800	Weak transcription	HSMM	muscle
8	chr15:42132200-42143400	Strong transcription	Fetal Muscle Leg	muscle
9	chr15:42136400-42146800	Weak transcription	Fetal Kidney	kidney
10	chr15:42138200-42173400	Weak transcription	Right Atrium	heart
11	chr15:42139200-42144000	Weak transcription	Colon Smooth Muscle	Colon
12	chr15:42139800-42143000	Strong transcription	HUVEC	blood vessel
13	chr15:42140400-42147800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:42140600-42143200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:42140600-42143200	Weak transcription	Primary B cells from cord blood	blood
16	chr15:42140800-42143200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr15:42140800-42144600	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr15:42141000-42143200	Enhancers	HMEC	breast
19	chr15:42141000-42143600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr15:42141000-42144000	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr15:42141000-42144400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:42141000-42146400	Enhancers	Fetal Lung	lung
23	chr15:42141000-42147200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:42141000-42147400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:42141000-42147600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:42141000-42149400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr15:42141000-42152200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr15:42141000-42154600	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:42141200-42143000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr15:42141200-42143000	Weak transcription	Ovary	ovary
31	chr15:42141200-42143200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:42141200-42143400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:42141200-42143600	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr15:42141200-42147000	Weak transcription	Fetal Thymus	thymus
35	chr15:42141200-42155200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr15:42141200-42191200	Weak transcription	Aorta	Aorta
37	chr15:42141400-42143000	Weak transcription	Brain Angular Gyrus	brain
38	chr15:42141400-42143000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:42141400-42143000	Weak transcription	Placenta	Placenta
40	chr15:42141400-42143000	Weak transcription	NHLF	lung
41	chr15:42141400-42143200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr15:42141400-42143600	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr15:42141400-42143800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr15:42141400-42144000	Weak transcription	Primary monocytes fromperipheralblood	blood
45	chr15:42141400-42145000	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:42141400-42152400	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr15:42141400-42155800	Weak transcription	HSMMtube	muscle
48	chr15:42141600-42143000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:42141600-42143600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:42141600-42143600	Weak transcription	Adipose Nuclei	Adipose

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