Variant report

Variant	rs11064873
Chromosome Location	chr12:120104992-120104993
allele	A/G
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	STAT5A	chr12:120104612-120105184	GM12878	blood:	n/a	n/a
2	BCL11A	chr12:120104697-120105058	GM12878	blood:	n/a	n/a
3	NFIC	chr12:120104029-120105869	GM12878	blood:	n/a	n/a
4	SP1	chr12:120104684-120105110	GM12878	blood:	n/a	n/a
5	SPI1	chr12:120104196-120105089	HL-60	blood:	n/a	chr12:120104436-120104449 chr12:120104562-120104571 chr12:120104438-120104447
6	REST	chr12:120104955-120106284	H1-neurons	neurons:	n/a	chr12:120105588-120105598
7	SPI1	chr12:120104086-120105263	GM12878	blood:	n/a	chr12:120104436-120104449 chr12:120104562-120104571 chr12:120104438-120104447
8	MXI1	chr12:120104725-120106494	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:120104827-120106232	Raji	blood:	n/a	n/a
10	EBF1	chr12:120104052-120105930	GM12878	blood:	n/a	n/a
11	SP1	chr12:120104641-120105169	GM12878	blood:	n/a	n/a
12	POU2F2	chr12:120104703-120105107	GM12878	blood:	n/a	chr12:120104927-120104940 chr12:120104926-120104940 chr12:120104929-120104939
13	TBP	chr12:120104291-120105989	GM12878	blood:	n/a	n/a
14	POLR2A	chr12:120104932-120105137	GM12891	blood:	n/a	n/a
15	FOS	chr12:120104674-120104997	HUVEC	blood vessel:	n/a	chr12:120104847-120104856 chr12:120104827-120104837 chr12:120104826-120104837 chr12:120104827-120104837
16	CEBPB	chr12:120104504-120105496	GM12878	blood:	n/a	chr12:120105118-120105129 chr12:120105116-120105129 chr12:120105116-120105129 chr12:120105118-120105129
17	SPI1	chr12:120104714-120105072	GM12891	blood:	n/a	n/a
18	RUNX3	chr12:120104607-120106235	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:120104759-120106596	GM12891	blood:	n/a	n/a
20	POU2F2	chr12:120104650-120105147	GM12878	blood:	n/a	chr12:120104927-120104940 chr12:120104678-120104691 chr12:120104926-120104940 chr12:120104668-120104690 chr12:120104929-120104939
21	BATF	chr12:120104625-120105015	GM12878	blood:	n/a	n/a
22	POU2F2	chr12:120104681-120105109	GM12891	blood:	n/a	chr12:120104927-120104940 chr12:120104926-120104940 chr12:120104929-120104939
23	SPI1	chr12:120104656-120105056	HL-60	blood:	n/a	n/a
24	SPI1	chr12:120104687-120105100	GM12891	blood:	n/a	n/a
25	FOXM1	chr12:120104856-120106126	GM12878	blood:	n/a	n/a
26	RELA	chr12:120104665-120105930	GM19099	blood:	n/a	n/a
27	GATA3	chr12:120104623-120105495	SH-SY5Y	brain:	n/a	chr12:120104822-120104829
28	ATF2	chr12:120104316-120106060	GM12878	blood:	n/a	n/a
29	PML	chr12:120104694-120105024	GM12878	blood:	n/a	n/a
30	BHLHE40	chr12:120104236-120106336	GM12878	blood:	n/a	chr12:120105590-120105606
31	GATA1	chr12:120104508-120106137	PBDE	blood:	n/a	chr12:120104822-120104829 chr12:120105994-120106004 chr12:120105836-120105844
32	NFIC	chr12:120104315-120105217	GM12878	blood:	n/a	n/a
33	MTA3	chr12:120104564-120106691	GM12878	blood:	n/a	n/a
34	BCLAF1	chr12:120104583-120105171	GM12878	blood:	n/a	n/a
35	RUNX3	chr12:120103990-120106155	GM12878	blood:	n/a	n/a
36	CHD2	chr12:120104761-120106098	GM12878	blood:	n/a	n/a
37	NFATC1	chr12:120104309-120105157	GM12878	blood:	n/a	n/a
38	GATA2	chr12:120104725-120105858	HUVEC	blood vessel:	n/a	chr12:120104822-120104829 chr12:120105836-120105844
39	RELA	chr12:120104694-120106197	GM18951	blood:	n/a	n/a
40	PML	chr12:120104352-120106743	GM12878	blood:	n/a	chr12:120106256-120106264
41	HCFC1	chr12:120104714-120106446	Hela-S3	cervix:	n/a	n/a
42	SIN3A	chr12:120104734-120106116	GM12878	blood:	n/a	chr12:120105550-120105563
43	FOXM1	chr12:120104349-120106302	GM12878	blood:	n/a	n/a
44	CTCF	chr12:120104578-120106752	A549	lung:	n/a	chr12:120105536-120105549 chr12:120105534-120105552 chr12:120105535-120105551
45	BATF	chr12:120104679-120105089	GM12878	blood:	n/a	n/a
46	EP300	chr12:120104659-120105244	GM12878	blood:	n/a	n/a
47	EP300	chr12:120104639-120106032	K562	blood:	n/a	chr12:120105668-120105682
48	MTA3	chr12:120104677-120105639	GM12878	blood:	n/a	n/a
49	TBL1XR1	chr12:120104215-120106103	GM12878	blood:	n/a	n/a
50	CTCF	chr12:120104984-120106183	SK-N-SH	brain:	n/a	chr12:120105536-120105549 chr12:120105534-120105552 chr12:120105535-120105551

No.	Distal block	Cell Line	Cell type
1	chr12:120103322..120105454-chr12:120505057..120506745,2	K562	blood:
2	chr12:120104659..120106467-chr4:174254824..174256542,2	MCF-7	breast:
3	chr12:119877799..119880484-chr12:120102287..120105032,2	K562	blood:
4	chr12:120104750..120107660-chr12:120111377..120114502,3	MCF-7	breast:
5	chr12:120104335..120107623-chr12:120110345..120114528,7	MCF-7	breast:
6	chr12:120085087..120087240-chr12:120102700..120105114,2	K562	blood:
7	chr12:120104565..120106668-chr12:120729361..120730960,2	K562	blood:

Variant related genes	Relation type
PRKAB1	TF binding region
ENSG00000111725	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000164104	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10849688	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10849690	1.00[ASN][1000 genomes]
rs175878	0.83[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978107	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1978108	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs278123	0.83[CEU][hapmap];0.88[GIH][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278126	0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs278143	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278144	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278145	0.83[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278147	0.83[CEU][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278148	0.83[CEU][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278149	0.83[CEU][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278151	0.83[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278152	0.83[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278154	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs278155	0.83[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3930004	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4213	0.83[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490266	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6490267	0.93[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304996	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310266	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7960723	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963248	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967558	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972600	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7979627	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs804667	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052595	chr12:119992580-120132038	Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv541616	chr12:119992580-120132038	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11064873	COQ5	cis	parietal	SCAN
rs11064873	PRKAB1	cis	cerebellum	SCAN
rs11064873	WSB2	cis	cerebellum	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:120100400-120105200	Weak transcription	Psoas Muscle	Psoas
2	chr12:120102200-120105200	Weak transcription	Aorta	Aorta
3	chr12:120102800-120105000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr12:120103600-120105000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:120103600-120105000	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr12:120103600-120105000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr12:120103600-120105000	Enhancers	Adipose Nuclei	Adipose
8	chr12:120103600-120105400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:120103600-120105400	Flanking Active TSS	GM12878-XiMat	blood
10	chr12:120103800-120105000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr12:120103800-120105200	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr12:120103800-120105400	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr12:120103800-120105400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr12:120103800-120105600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr12:120104000-120105200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr12:120104000-120105200	Weak transcription	Placenta	Placenta
17	chr12:120104000-120105200	Weak transcription	Spleen	Spleen
18	chr12:120104000-120105400	Flanking Active TSS	Primary hematopoietic stem cells	blood
19	chr12:120104200-120105000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:120104200-120105400	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr12:120104200-120105400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr12:120104200-120105400	Flanking Active TSS	Dnd41	blood
23	chr12:120104400-120105000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr12:120104400-120105000	Enhancers	Fetal Kidney	kidney
25	chr12:120104600-120105000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr12:120104600-120105000	Enhancers	Liver	Liver
27	chr12:120104600-120105000	Enhancers	Fetal Brain Female	brain
28	chr12:120104600-120105000	Enhancers	Fetal Lung	lung
29	chr12:120104600-120105000	Enhancers	Osteobl	bone
30	chr12:120104600-120105400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
31	chr12:120104800-120105000	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr12:120104800-120105000	Active TSS	HUES64 Cell Line	embryonic stem cell
33	chr12:120104800-120105000	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr12:120104800-120105000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr12:120104800-120105000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr12:120104800-120105000	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr12:120104800-120105000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr12:120104800-120105000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:120104800-120105000	Enhancers	Muscle Satellite Cultured Cells	--
40	chr12:120104800-120105000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr12:120104800-120105000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr12:120104800-120105000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:120104800-120105000	Flanking Active TSS	Brain Anterior Caudate	brain
44	chr12:120104800-120105000	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr12:120104800-120105000	Active TSS	Fetal Brain Male	brain
46	chr12:120104800-120105000	Enhancers	Fetal Heart	heart
47	chr12:120104800-120105000	Enhancers	Fetal Intestine Small	intestine
48	chr12:120104800-120105000	Enhancers	Pancreatic Islets	Pancreatic Islet
49	chr12:120104800-120105000	Enhancers	Fetal Muscle Leg	muscle
50	chr12:120104800-120105000	Enhancers	Fetal Stomach	stomach

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