Variant report

Variant	rs880369
Chromosome Location	chr12:9517550-9517551
allele	C/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	POLR2A	chr12:9516729-9517905	GM12878	blood:	n/a	n/a
2	BATF	chr12:9516696-9517884	GM12878	blood:	n/a	n/a
3	MEF2A	chr12:9516791-9518262	GM12878	blood:	n/a	n/a
4	TBP	chr12:9516919-9518117	GM12878	blood:	n/a	n/a
5	MXI1	chr12:9516988-9517917	GM12878	blood:	n/a	n/a
6	POU2F2	chr12:9516664-9517787	GM12891	blood:	n/a	n/a
7	POLR2A	chr12:9516672-9518064	U87	brain:	n/a	n/a
8	BCL11A	chr12:9516825-9517859	GM12878	blood:	n/a	n/a
9	TBL1XR1	chr12:9515537-9518036	GM12878	blood:	n/a	n/a
10	SRF	chr12:9516956-9517842	GM12878	blood:	n/a	n/a
11	FOS	chr12:9517442-9518153	MCF10A-Er-Src	breast:	n/a	n/a
12	EP300	chr12:9516766-9517567	GM12878	blood:	n/a	n/a
13	MEF2C	chr12:9516773-9517829	GM12878	blood:	n/a	n/a
14	JUND	chr12:9516829-9518060	GM12878	blood:	n/a	chr12:9517603-9517614
15	MAX	chr12:9516965-9517905	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:9515357-9518289	GM12891	blood:	n/a	n/a
17	RFX5	chr12:9516836-9517768	GM12878	blood:	n/a	n/a
18	MTA3	chr12:9513806-9518741	GM12878	blood:	n/a	n/a
19	CHD2	chr12:9516713-9518340	GM12878	blood:	n/a	n/a
20	NFIC	chr12:9516412-9518439	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:9515210-9518678	GM12892	blood:	n/a	n/a
22	RCOR1	chr12:9516850-9517788	GM12878	blood:	n/a	n/a
23	SP1	chr12:9516881-9517839	GM12878	blood:	n/a	n/a
24	POU2F2	chr12:9516681-9517838	GM12891	blood:	n/a	n/a
25	MAZ	chr12:9516915-9517907	GM12878	blood:	n/a	n/a
26	JUND	chr12:9517032-9517755	H1-hESC	embryonic stem cell:	n/a	chr12:9517603-9517614
27	MYC	chr12:9517385-9517902	MCF10A-Er-Src	breast:	n/a	n/a
28	EBF1	chr12:9516711-9518338	GM12878	blood:	n/a	n/a
29	POLR2A	chr12:9516654-9517618	HL-60	blood:	n/a	n/a
30	POLR2A	chr12:9515459-9518442	GM12891	blood:	n/a	n/a
31	FOS	chr12:9517423-9518083	MCF10A-Er-Src	breast:	n/a	n/a
32	E2F4	chr12:9517130-9517690	GM12878	blood:	n/a	n/a
33	CREB1	chr12:9516804-9517992	GM12878	blood:	n/a	n/a
34	JUND	chr12:9516950-9517793	K562	blood:	n/a	chr12:9517603-9517614
35	POLR2A	chr12:9516640-9517971	GM12892	blood:	n/a	n/a
36	STAT5A	chr12:9516488-9518089	GM12878	blood:	n/a	chr12:9516641-9516655 chr12:9516596-9516607
37	POU2F2	chr12:9516631-9517814	GM12878	blood:	n/a	n/a
38	ATF2	chr12:9514144-9518351	GM12878	blood:	n/a	n/a
39	TCF3	chr12:9516917-9517689	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:9516711-9517890	U87	brain:	n/a	n/a
41	YY1	chr12:9516758-9517963	GM12878	blood:	n/a	n/a
42	POLR2A	chr12:9515268-9518663	GM12892	blood:	n/a	n/a
43	EP300	chr12:9516474-9517863	GM12878	blood:	n/a	n/a
44	FOS	chr12:9517449-9517807	MCF10A-Er-Src	breast:	n/a	n/a
45	POLR2A	chr12:9516444-9517946	GM12891	blood:	n/a	n/a
46	EP300	chr12:9516683-9518190	GM12878	blood:	n/a	chr12:9517986-9518000 chr12:9517985-9517999 chr12:9517987-9518001 chr12:9517984-9517998
47	POLR2A	chr12:9516220-9517950	GM12891	blood:	n/a	n/a
48	RUNX3	chr12:9516224-9518329	GM12878	blood:	n/a	n/a
49	BCLAF1	chr12:9516321-9518443	GM12878	blood:	n/a	n/a
50	MEF2A	chr12:9516690-9518027	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9516871..9518767-chr12:9528942..9530878,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260423	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10743683	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs10743685	0.80[ASN][1000 genomes]
rs1076524	0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11050535	0.83[ASN][1000 genomes]
rs11612935	0.85[ASN][1000 genomes]
rs12320763	0.94[ASW][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1549432	0.85[ASN][1000 genomes]
rs1549433	0.85[ASN][1000 genomes]
rs17732137	0.85[ASN][1000 genomes]
rs2003608	0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs28735913	0.85[ASN][1000 genomes]
rs4882995	0.82[ASN][1000 genomes]
rs4883248	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs66778915	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs68104378	0.83[ASN][1000 genomes]
rs7297302	0.86[ASN][1000 genomes]
rs7300552	0.93[ASN][1000 genomes]
rs7310818	1.00[JPT][hapmap]
rs7958583	0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:20 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045317	chr12:9113216-9544655	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
2	nsv1048491	chr12:9208806-9544655	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv523958	chr12:9303440-9549072	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
4	nsv557355	chr12:9309995-9529015	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1035953	chr12:9314481-9544655	Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
7	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
8	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
9	nsv916832	chr12:9397450-9693952	ZNF genes & repeats Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv976736	chr12:9431362-9524845	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv898740	chr12:9436446-9546962	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv1050161	chr12:9436635-9685768	Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
13	nsv898741	chr12:9458525-9546962	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
14	nsv1035958	chr12:9472365-9579109	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active 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	11 gene(s)	inside rSNPs	diseases
15	nsv898742	chr12:9473157-9518222	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
16	nsv898743	chr12:9473157-9522350	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
17	nsv975403	chr12:9481646-9541991	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	esv3436788	chr12:9499151-9519686	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
19	esv3332298	chr12:9500121-9519487	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
20	esv2760260	chr12:9504060-9519172	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs880369	VWF	cis	cerebellum	SCAN
rs880369	KLRC4	cis	cerebellum	SCAN
rs880369	NECAP1	cis	parietal	SCAN
rs880369	KLRC4	cis	parietal	SCAN
rs880369	ANO2	cis	cerebellum	SCAN

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9515000-9517800	Weak transcription	Primary neutrophils fromperipheralblood	blood
2	chr12:9515400-9519200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:9515600-9518600	Enhancers	Primary B cells from peripheral blood	blood
4	chr12:9515800-9518200	Enhancers	HSMMtube	muscle
5	chr12:9515800-9518600	Enhancers	H9 Cell Line	embryonic stem cell
6	chr12:9515800-9520000	Enhancers	H1 Cell Line	embryonic stem cell
7	chr12:9515800-9520000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr12:9516000-9518400	Enhancers	Primary hematopoietic stem cells short term culture	blood
9	chr12:9516000-9518400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:9516000-9519800	Weak transcription	Right Atrium	heart
11	chr12:9516000-9521200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:9516200-9518000	Enhancers	Brain Germinal Matrix	brain
13	chr12:9516400-9518400	Enhancers	Brain Angular Gyrus	brain
14	chr12:9516400-9520000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr12:9516600-9518000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr12:9516600-9518000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr12:9516600-9518400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr12:9516600-9520000	Enhancers	Fetal Stomach	stomach
19	chr12:9516800-9517600	Enhancers	Fetal Muscle Trunk	muscle
20	chr12:9516800-9517600	Enhancers	Ovary	ovary
21	chr12:9516800-9517800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
22	chr12:9516800-9517800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr12:9516800-9518000	Flanking Active TSS	HepG2	liver
24	chr12:9516800-9518000	Flanking Active TSS	NH-A	brain
25	chr12:9516800-9518200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr12:9516800-9518400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:9516800-9518600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:9516800-9518600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr12:9516800-9520000	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr12:9516800-9520400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr12:9516800-9520600	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr12:9516800-9521600	Enhancers	Fetal Lung	lung
33	chr12:9517000-9517600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
34	chr12:9517000-9517800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr12:9517000-9517800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
36	chr12:9517000-9517800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr12:9517000-9517800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr12:9517000-9518000	Enhancers	Brain Substantia Nigra	brain
39	chr12:9517000-9518200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr12:9517000-9518200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr12:9517000-9518200	Flanking Active TSS	HMEC	breast
42	chr12:9517000-9518200	Flanking Active TSS	Osteobl	bone
43	chr12:9517000-9518400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr12:9517000-9518600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:9517200-9517600	Active TSS	ES-I3 Cell Line	embryonic stem cell
46	chr12:9517200-9517600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:9517200-9517600	Enhancers	Primary B cells from cord blood	blood
48	chr12:9517200-9517600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
49	chr12:9517200-9517600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
50	chr12:9517200-9517600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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