Variant report

Variant	rs10459592
Chromosome Location	chr15:51536141-51536142
allele	G/T
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	JUND	chr15:51536048-51536191	HepG2	liver:	n/a	chr15:51536150-51536161 chr15:51536152-51536163 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
2	FOSL2	chr15:51536003-51536321	HepG2	liver:	n/a	chr15:51536150-51536161 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163 chr15:51536153-51536164
3	CBX3	chr15:51535736-51536386	HCT-116	colon:	n/a	n/a
4	MAFK	chr15:51535980-51536308	HepG2	liver:	n/a	chr15:51536155-51536164
5	FOS	chr15:51535936-51536362	MCF10A-Er-Src	breast:	n/a	chr15:51536150-51536161 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
6	JUND	chr15:51535929-51536345	K562	blood:	n/a	chr15:51536150-51536161 chr15:51536152-51536163 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
7	MYC	chr15:51536015-51536277	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr15:51535966-51536343	MCF10A-Er-Src	breast:	n/a	chr15:51536150-51536161 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
9	SP1	chr15:51535881-51536446	HCT-116	colon:	n/a	n/a
10	JUN	chr15:51536015-51536335	HepG2	liver:	n/a	chr15:51536150-51536161 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
11	JUND	chr15:51535980-51536405	Hela-S3	cervix:	n/a	chr15:51536150-51536161 chr15:51536152-51536163 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
12	RUNX3	chr15:51535923-51536324	GM12878	blood:	n/a	n/a
13	JUND	chr15:51535785-51536528	MCF-7	breast:	n/a	chr15:51536150-51536161 chr15:51536152-51536163 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
14	JUN	chr15:51535968-51536219	H1-hESC	embryonic stem cell:	n/a	chr15:51536150-51536161 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
15	JUND	chr15:51535829-51536421	HCT-116	colon:	n/a	chr15:51536150-51536161 chr15:51536152-51536163 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
16	FOSL1	chr15:51535724-51536486	HCT-116	colon:	n/a	chr15:51536150-51536161 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
17	FOSL2	chr15:51535847-51536472	MCF-7	breast:	n/a	chr15:51536150-51536161 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163 chr15:51536153-51536164
18	FOSL2	chr15:51535915-51536339	HepG2	liver:	n/a	chr15:51536150-51536161 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163 chr15:51536153-51536164
19	FOS	chr15:51535964-51536341	MCF10A-Er-Src	breast:	n/a	chr15:51536150-51536161 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
20	JUND	chr15:51535871-51536431	SK-N-SH	brain:	n/a	chr15:51536150-51536161 chr15:51536152-51536163 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
21	STAT3	chr15:51536008-51536239	MCF10A-Er-Src	breast:	n/a	chr15:51536154-51536163 chr15:51536071-51536094
22	STAT3	chr15:51535900-51536207	MCF10A-Er-Src	breast:	n/a	chr15:51536154-51536163 chr15:51536071-51536094
23	FOS	chr15:51535969-51536279	HUVEC	blood vessel:	n/a	chr15:51536150-51536161 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
24	NFATC1	chr15:51535895-51536369	GM12878	blood:	n/a	n/a
25	JUND	chr15:51535788-51536407	HCT-116	colon:	n/a	chr15:51536150-51536161 chr15:51536152-51536163 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
26	KAP1	chr15:51535902-51536381	U2OS	brain:	n/a	chr15:51536155-51536164
27	SP1	chr15:51535772-51536401	HCT-116	colon:	n/a	n/a
28	NFIC	chr15:51535848-51536361	GM12878	blood:	n/a	n/a
29	POLR2A	chr15:51535970-51536320	HCT-116	colon:	n/a	n/a
30	JUND	chr15:51535756-51536476	MCF-7	breast:	n/a	chr15:51536150-51536161 chr15:51536152-51536163 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
31	STAT3	chr15:51536097-51536251	MCF10A-Er-Src	breast:	n/a	chr15:51536154-51536163
32	MAFK	chr15:51536044-51536299	HepG2	liver:	n/a	chr15:51536155-51536164
33	BATF	chr15:51536007-51536277	GM12878	blood:	n/a	chr15:51536154-51536165
34	ATF1	chr15:51536044-51536212	K562	blood:	n/a	n/a
35	MAFF	chr15:51536061-51536261	K562	blood:	n/a	n/a
36	JUND	chr15:51535976-51536328	H1-hESC	embryonic stem cell:	n/a	chr15:51536150-51536161 chr15:51536152-51536163 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
37	JUND	chr15:51535970-51536341	HepG2	liver:	n/a	chr15:51536150-51536161 chr15:51536152-51536163 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
38	MAFK	chr15:51536006-51536257	K562	blood:	n/a	chr15:51536155-51536164
39	MYC	chr15:51536009-51536211	MCF10A-Er-Src	breast:	n/a	n/a
40	JUN	chr15:51535937-51536488	K562	blood:	n/a	chr15:51536150-51536161 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163
41	FOSL2	chr15:51535878-51536457	MCF-7	breast:	n/a	chr15:51536150-51536161 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163 chr15:51536153-51536164
42	FOSL1	chr15:51535932-51536448	HCT-116	colon:	n/a	chr15:51536150-51536161 chr15:51536155-51536162 chr15:51536153-51536163 chr15:51536152-51536164 chr15:51536153-51536163 chr15:51536153-51536162 chr15:51536154-51536163

No.	Distal block	Cell Line	Cell type
1	chr15:51535935..51537605-chr15:51539131..51540718,2	MCF-7	breast:
2	chr15:51534794..51537760-chr15:51568479..51570855,2	MCF-7	breast:
3	chr15:51533024..51534733-chr15:51535544..51538470,2	K562	blood:

Variant related genes	Relation type
CYP19A1	TF binding region
ENSG00000137869	Chromatin interaction
ENSG00000266593	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10519297	0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1062033	0.82[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1065778	0.83[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10851498	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10851499	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632036	0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs11633715	0.88[ASN][1000 genomes]
rs11636403	0.85[JPT][hapmap]
rs11636667	0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs11636686	0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs12050772	0.82[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12899068	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900487	0.83[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12901187	0.85[JPT][hapmap]
rs12907866	0.82[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs12908960	0.82[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs17523270	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs17523284	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs2414096	0.89[ASN][1000 genomes]
rs2414098	0.83[EUR][1000 genomes]
rs35241865	0.88[ASN][1000 genomes]
rs35808887	0.88[ASN][1000 genomes]
rs3759811	0.82[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4775936	1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs56097510	0.90[ASN][1000 genomes]
rs61018102	0.90[ASN][1000 genomes]
rs6493494	0.85[JPT][hapmap]
rs700518	0.83[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs7176330	0.89[ASN][1000 genomes]
rs767199	0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs8041967	0.90[JPT][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
3	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
4	nsv1049644	chr15:51265447-51560445	Strong transcription Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
5	esv34532	chr15:51276128-51752856	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	esv2758382	chr15:51282257-51830339	Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv2760031	chr15:51282257-51830339	Weak transcription Enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	esv2757600	chr15:51352249-51783981	Weak transcription Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10459592	TMOD2	cis	cerebellum	SCAN
rs10459592	TRPM7	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51524800-51574000	Weak transcription	HepG2	liver
2	chr15:51533400-51536400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:51533600-51542200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr15:51533800-51537400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:51534000-51542000	Strong transcription	Placenta	Placenta
6	chr15:51534800-51537600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr15:51535400-51536800	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr15:51535400-51538200	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr15:51535800-51536200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr15:51535800-51536200	Enhancers	Ovary	ovary
11	chr15:51535800-51536200	Enhancers	NHEK	skin
12	chr15:51535800-51536400	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr15:51535800-51536400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:51535800-51536400	Enhancers	HMEC	breast
15	chr15:51535800-51537000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr15:51535800-51537000	Enhancers	Muscle Satellite Cultured Cells	--
17	chr15:51536000-51536200	Flanking Active TSS	GM12878-XiMat	blood
18	chr15:51536000-51536400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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