Variant report

Variant	rs1805754
Chromosome Location	chr12:9103248-9103249
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	MAX	chr12:9101328-9103384	GM12878	blood:	n/a	n/a
2	BRCA1	chr12:9102304-9103330	H1-hESC	embryonic stem cell:	n/a	n/a
3	MXI1	chr12:9101469-9103384	Hela-S3	cervix:	n/a	chr12:9102579-9102588
4	POLR2A	chr12:9101430-9103328	SK-N-MC	brain:	n/a	n/a
5	MYC	chr12:9101994-9103474	MCF10A-Er-Src	breast:	n/a	n/a
6	MYC	chr12:9101299-9103326	NB4	blood:	n/a	n/a
7	MAX	chr12:9101323-9103541	NB4	blood:	n/a	n/a
8	MAX	chr12:9101765-9103309	HepG2	liver:	n/a	n/a
9	GTF2F1	chr12:9101592-9103558	Hela-S3	cervix:	n/a	n/a
10	MYC	chr12:9101502-9103460	Hela-S3	cervix:	n/a	n/a
11	MAFK	chr12:9102510-9103252	K562	blood:	n/a	n/a
12	RFX5	chr12:9101581-9103502	Hela-S3	cervix:	n/a	chr12:9102269-9102283 chr12:9102369-9102378
13	GABPA	chr12:9101619-9103260	MCF-7	breast:	n/a	chr12:9102592-9102599 chr12:9103181-9103188
14	RELA	chr12:9101752-9103382	GM19193	blood:	n/a	n/a
15	ZNF143	chr12:9101426-9103352	K562	blood:	n/a	chr12:9102633-9102642 chr12:9102624-9102642 chr12:9102631-9102640
16	MAX	chr12:9101781-9103293	A549	lung:	n/a	n/a
17	BHLHE40	chr12:9102999-9103276	A549	lung:	n/a	n/a
18	SIN3A	chr12:9101247-9103369	H1-hESC	embryonic stem cell:	n/a	n/a
19	RELA	chr12:9101411-9103320	GM18951	blood:	n/a	n/a
20	CTCF	chr12:9101625-9103881	A549	lung:	n/a	chr12:9102284-9102297
21	TBL1XR1	chr12:9101530-9103316	K562	blood:	n/a	n/a
22	CTCF	chr12:9101386-9103984	SK-N-SH	brain:	n/a	chr12:9102284-9102297
23	WRNIP1	chr12:9100991-9103253	GM12878	blood:	n/a	n/a
24	MAX	chr12:9101764-9103314	ECC-1	luminal epithelium:	n/a	n/a
25	MAZ	chr12:9101880-9103382	GM12878	blood:	n/a	n/a
26	POLR2A	chr12:9101283-9103486	Hela-S3	cervix:	n/a	n/a
27	TBP	chr12:9101646-9103248	Hela-S3	cervix:	n/a	n/a
28	POLR2A	chr12:9100949-9103269	MCF10A-Er-Src	breast:	n/a	n/a
29	CHD1	chr12:9102395-9103416	H1-hESC	embryonic stem cell:	n/a	chr12:9102993-9103000
30	GABPA	chr12:9101818-9103277	A549	lung:	n/a	chr12:9102592-9102599 chr12:9103181-9103188
31	CHD2	chr12:9101448-9103364	Hela-S3	cervix:	n/a	chr12:9102993-9103000
32	MAX	chr12:9101910-9103250	HepG2	liver:	n/a	n/a
33	GATA2	chr12:9101382-9104014	SH-SY5Y	brain:	n/a	chr12:9101452-9101462 chr12:9101841-9101852
34	RCOR1	chr12:9101604-9103318	Hela-S3	cervix:	n/a	n/a
35	MXI1	chr12:9101515-9103257	GM12878	blood:	n/a	chr12:9102579-9102588
36	IRF1	chr12:9101572-9103880	K562	blood:	n/a	chr12:9103658-9103671 chr12:9103656-9103670 chr12:9103660-9103671 chr12:9103659-9103676 chr12:9103658-9103671 chr12:9103660-9103670 chr12:9103658-9103671 chr12:9103661-9103672 chr12:9103761-9103774 chr12:9102370-9102379 chr12:9102242-9102262
37	HCFC1	chr12:9101198-9103534	Hela-S3	cervix:	n/a	n/a
38	MXI1	chr12:9101035-9104283	SK-N-SH	brain:	n/a	chr12:9102579-9102588
39	POLR2A	chr12:9101410-9103347	K562	blood:	n/a	n/a
40	EP300	chr12:9101469-9103603	K562	blood:	n/a	chr12:9102819-9102828
41	MXI1	chr12:9101119-9103770	IMR90	lung:	n/a	chr12:9102579-9102588
42	MYC	chr12:9101299-9103659	K562	blood:	n/a	n/a
43	MAZ	chr12:9101373-9103399	K562	blood:	n/a	n/a
44	POLR2A	chr12:9101700-9103287	HepG2	liver:	n/a	n/a
45	MYC	chr12:9101283-9103358	K562	blood:	n/a	n/a
46	GATA1	chr12:9101314-9103992	PBDE	blood:	n/a	chr12:9101452-9101462 chr12:9101841-9101852

No.	Distal block	Cell Line	Cell type
1	chr12:8850179..8851815-chr12:9101960..9104335,2	MCF-7	breast:
2	chr12:9065401..9068009-chr12:9098811..9103435,5	MCF-7	breast:
3	chr12:8831240..8834725-chr12:9101135..9103936,3	MCF-7	breast:
4	chr12:9103173..9107180-chr12:9112850..9116183,4	K562	blood:
5	chr12:9093611..9096195-chr12:9102368..9104030,2	K562	blood:
6	chr12:9097804..9100498-chr12:9103089..9104894,4	K562	blood:
7	chr12:8849018..8850959-chr12:9102785..9104647,2	K562	blood:
8	chr12:8849223..8851082-chr12:9101432..9104201,2	K562	blood:
9	chr12:9093100..9096905-chr12:9100746..9103868,4	K562	blood:
10	chr12:9081265..9083698-chr12:9100850..9103403,2	MCF-7	breast:
11	chr12:9100379..9103293-chr12:9215519..9218225,4	MCF-7	breast:
12	chr12:9103173..9105935-chr12:9114683..9116241,2	K562	blood:
13	chr12:9096830..9100498-chr12:9102068..9104762,4	K562	blood:

Variant related genes	Relation type
M6PR	TF binding region
ENSG00000214851	Chromatin interaction
ENSG00000003056	Chromatin interaction
ENSG00000166532	Chromatin interaction
ENSG00000111752	Chromatin interaction
ENSG00000245105	Chromatin interaction
ENSG00000256004	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10129061	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10400516	0.81[ASN][1000 genomes]
rs10400563	0.83[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs10743568	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10771238	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11048190	0.84[ASN][1000 genomes]
rs11048195	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs11048264	0.81[ASN][1000 genomes]
rs11048337	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs11048338	0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs11048344	0.83[ASN][1000 genomes]
rs11048345	0.83[ASN][1000 genomes]
rs1121401	0.85[ASN][1000 genomes]
rs11614202	0.88[ASN][1000 genomes]
rs12423746	0.83[ASN][1000 genomes]
rs12423817	0.83[ASN][1000 genomes]
rs12424026	0.83[ASN][1000 genomes]
rs12812913	0.83[ASN][1000 genomes]
rs12821842	0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs12823100	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs12833375	0.83[ASN][1000 genomes]
rs1476911	0.91[CHB][hapmap]
rs1805248	1.00[CHB][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1805724	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs1805725	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.88[ASN][1000 genomes]
rs1805727	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.87[ASN][1000 genomes]
rs1805732	0.91[CHB][hapmap]
rs1805733	0.91[CHB][hapmap]
rs1805735	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs1805761	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs1805765	0.82[CHB][hapmap]
rs2041624	0.83[ASN][1000 genomes]
rs2041625	0.83[ASN][1000 genomes]
rs2284349	0.94[JPT][hapmap]
rs2377671	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2377672	0.82[ASN][1000 genomes]
rs2377673	0.83[ASN][1000 genomes]
rs2377674	0.83[ASN][1000 genomes]
rs2377676	0.85[ASN][1000 genomes]
rs34798934	0.83[ASN][1000 genomes]
rs4309200	0.95[CHB][hapmap];0.84[CHD][hapmap];0.83[ASN][1000 genomes]
rs4639983	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4883203	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6832	0.95[CHB][hapmap]
rs7132930	0.83[ASN][1000 genomes]
rs7300767	0.83[ASN][1000 genomes]
rs7301381	0.81[ASN][1000 genomes]
rs7957321	0.83[ASN][1000 genomes]
rs7961355	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7974486	0.85[ASN][1000 genomes]
rs887782	0.82[GIH][hapmap]
rs933462	0.95[CHB][hapmap];0.84[ASN][1000 genomes]
rs987917	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1805754	M6PR	cis	lung	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9099400-9103600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr12:9099600-9103600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:9100200-9103400	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr12:9100200-9103800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:9100200-9103800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:9100400-9103600	Active TSS	HSMMtube	muscle
7	chr12:9100400-9103800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr12:9100400-9103800	Active TSS	Right Atrium	heart
9	chr12:9100400-9103800	Active TSS	K562	blood
10	chr12:9100400-9104000	Active TSS	GM12878-XiMat	blood
11	chr12:9100600-9103800	Active TSS	NHLF	lung
12	chr12:9100800-9103400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:9100800-9103600	Active TSS	H1 Cell Line	embryonic stem cell
14	chr12:9101000-9103400	Active TSS	iPS-18 Cell Line	embryonic stem cell
15	chr12:9101000-9103400	Active TSS	Breast Myoepithelial Primary Cells	Breast
16	chr12:9101000-9103600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:9101000-9103600	Active TSS	HUES48 Cell Line	embryonic stem cell
18	chr12:9101000-9103600	Active TSS	Fetal Intestine Small	intestine
19	chr12:9101000-9103600	Active TSS	Right Ventricle	heart
20	chr12:9101000-9103600	Active TSS	HSMM	muscle
21	chr12:9101000-9103800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr12:9101000-9103800	Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr12:9101000-9103800	Active TSS	Fetal Intestine Large	intestine
24	chr12:9101000-9104000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:9101000-9104400	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr12:9101200-9103400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
27	chr12:9101200-9103400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr12:9101200-9103400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:9101200-9103400	Active TSS	HUES64 Cell Line	embryonic stem cell
30	chr12:9101200-9103400	Active TSS	iPS-15b Cell Line	embryonic stem cell
31	chr12:9101200-9103400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr12:9101200-9103400	Active TSS	Primary monocytes fromperipheralblood	blood
33	chr12:9101200-9103400	Active TSS	Fetal Kidney	kidney
34	chr12:9101200-9103400	Active TSS	Fetal Muscle Trunk	muscle
35	chr12:9101200-9103400	Active TSS	Ovary	ovary
36	chr12:9101200-9103400	Active TSS	Hela-S3	cervix
37	chr12:9101200-9103600	Active TSS	H9 Cell Line	embryonic stem cell
38	chr12:9101200-9103600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr12:9101200-9103600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:9101200-9103600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr12:9101200-9103600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:9101200-9103600	Active TSS	Colonic Mucosa	Colon
43	chr12:9101200-9103600	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr12:9101200-9103600	Active TSS	NHDF-Ad	bronchial
45	chr12:9101200-9103800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:9101200-9103800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr12:9101200-9103800	Active TSS	Muscle Satellite Cultured Cells	--
48	chr12:9101200-9103800	Active TSS	Left Ventricle	heart
49	chr12:9101200-9103800	Active TSS	HMEC	breast
50	chr12:9101200-9104000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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