Variant report

Variant	rs1805757
Chromosome Location	chr12:9101620-9101621
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	MAX	chr12:9101328-9103384	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:9101509-9101652	HepG2	liver:	n/a	n/a
3	YY1	chr12:9101266-9101740	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:9101227-9102955	GM12892	blood:	n/a	n/a
5	POLR2A	chr12:9101199-9103047	GM12892	blood:	n/a	n/a
6	POLR2A	chr12:9101100-9103207	GM12891	blood:	n/a	n/a
7	MXI1	chr12:9101469-9103384	Hela-S3	cervix:	n/a	chr12:9102579-9102588
8	POLR2A	chr12:9101212-9102938	GM12891	blood:	n/a	n/a
9	POLR2A	chr12:9101430-9103328	SK-N-MC	brain:	n/a	n/a
10	MYC	chr12:9101299-9103326	NB4	blood:	n/a	n/a
11	MYC	chr12:9101593-9101701	K562	blood:	n/a	n/a
12	CHD2	chr12:9101301-9103109	GM12878	blood:	n/a	chr12:9102993-9103000
13	POLR2A	chr12:9101391-9103109	NB4	blood:	n/a	n/a
14	MAX	chr12:9101323-9103541	NB4	blood:	n/a	n/a
15	REST	chr12:9101555-9103129	H1-neurons	neurons:	n/a	chr12:9102542-9102552 chr12:9102697-9102704 chr12:9102220-9102233
16	POLR2A	chr12:9101566-9102922	HepG2	liver:	n/a	n/a
17	POLR2A	chr12:9101334-9102999	GM18505	blood:	n/a	n/a
18	POLR2A	chr12:9101359-9103136	HepG2	liver:	n/a	n/a
19	MXI1	chr12:9101437-9103026	H1-hESC	embryonic stem cell:	n/a	chr12:9102579-9102588
20	YY1	chr12:9101485-9101792	GM12891	blood:	n/a	n/a
21	POLR2A	chr12:9101603-9102865	MCF-7	breast:	n/a	n/a
22	USF2	chr12:9101409-9103129	H1-hESC	embryonic stem cell:	n/a	chr12:9102304-9102315
23	POLR2A	chr12:9101049-9103146	MCF10A-Er-Src	breast:	n/a	n/a
24	GTF2F1	chr12:9101592-9103558	Hela-S3	cervix:	n/a	n/a
25	ELF1	chr12:9101377-9101741	K562	blood:	n/a	n/a
26	POLR2A	chr12:9101513-9101656	ProgFib	skin:	n/a	n/a
27	MYC	chr12:9101502-9103460	Hela-S3	cervix:	n/a	n/a
28	TBP	chr12:9101579-9103079	HepG2	liver:	n/a	n/a
29	TBL1XR1	chr12:9101534-9103228	GM12878	blood:	n/a	n/a
30	POLR2A	chr12:9101381-9102994	Hela-S3	cervix:	n/a	n/a
31	RFX5	chr12:9101581-9103502	Hela-S3	cervix:	n/a	chr12:9102269-9102283 chr12:9102369-9102378
32	HCFC1	chr12:9101323-9101651	K562	blood:	n/a	n/a
33	IRF1	chr12:9100899-9103127	K562	blood:	n/a	chr12:9101236-9101248 chr12:9101237-9101247 chr12:9101235-9101255 chr12:9101237-9101251 chr12:9101236-9101248 chr12:9101367-9101376 chr12:9102370-9102379 chr12:9102242-9102262 chr12:9101236-9101250 chr12:9101111-9101120
34	GABPA	chr12:9101619-9103260	MCF-7	breast:	n/a	chr12:9102592-9102599 chr12:9103181-9103188
35	POLR2A	chr12:9101453-9103130	GM19099	blood:	n/a	n/a
36	POLR2A	chr12:9101538-9101644	HUVEC	blood vessel:	n/a	n/a
37	MAX	chr12:9101548-9103115	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr12:9101459-9103226	HUVEC	blood vessel:	n/a	n/a
39	STAT3	chr12:9101482-9101912	MCF10A-Er-Src	breast:	n/a	chr12:9101776-9101784
40	POLR2A	chr12:9101248-9103044	HL-60	blood:	n/a	n/a
41	SMARCC1	chr12:9101288-9103143	Hela-S3	cervix:	n/a	chr12:9102633-9102642
42	SPI1	chr12:9101239-9101639	GM12891	blood:	n/a	chr12:9101370-9101379 chr12:9101368-9101381
43	POLR2A	chr12:9101422-9102905	GM12891	blood:	n/a	n/a
44	ZNF143	chr12:9101426-9103352	K562	blood:	n/a	chr12:9102633-9102642 chr12:9102624-9102642 chr12:9102631-9102640
45	ZMIZ1	chr12:9101357-9102985	K562	blood:	n/a	n/a
46	POLR2A	chr12:9101208-9103006	GM12878	blood:	n/a	n/a
47	MAFK	chr12:9101344-9102033	K562	blood:	n/a	n/a
48	YY1	chr12:9101286-9101754	K562	blood:	n/a	n/a
49	SIN3A	chr12:9101247-9103369	H1-hESC	embryonic stem cell:	n/a	n/a
50	CHD1	chr12:9101599-9102179	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:53685799..53686542-chr12:9101282..9102188,2	Hela-S3	cervix:
2	chr12:9064351..9068260-chr12:9100706..9102986,3	MCF-7	breast:
3	chr12:9086089..9087929-chr12:9099669..9102471,2	MCF-7	breast:
4	chr12:9065401..9068009-chr12:9098811..9103435,5	MCF-7	breast:
5	chr12:8831240..8834725-chr12:9101135..9103936,3	MCF-7	breast:
6	chr12:9066826..9070397-chr12:9099293..9102558,3	K562	blood:
7	chr12:9083802..9086315-chr12:9099049..9101665,2	MCF-7	breast:
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	chr12:9101375..9101963-chr3:156877437..156878258,2	Hela-S3	cervix:
12	chr12:9100379..9103293-chr12:9215519..9218225,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-A2M-3	chr12:9101483-9101926	ucscGeneNc_uc009zgh_1

Variant related genes	Relation type
KLRG1	TF binding region
M6PR	TF binding region
ENSG00000166532	Chromatin interaction
ENSG00000245105	Chromatin interaction
ENSG00000256004	Chromatin interaction
ENSG00000163660	Chromatin interaction
ENSG00000259818	Chromatin interaction
ENSG00000111752	Chromatin interaction
ENSG00000214851	Chromatin interaction
ENSG00000003056	Chromatin interaction
ENSG00000162384	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11047080	1.00[TSI][hapmap]
rs11836936	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs1805755	1.00[ASW][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1805763	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3026262	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs56699774	0.95[AFR][1000 genomes]
rs56808213	0.82[AFR][1000 genomes]
rs57343883	0.82[AFR][1000 genomes]
rs61495555	0.86[AFR][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

No data

Chromatin state (count:127 , 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	chr12:9100000-9101800	Flanking Active TSS	Primary T cells from cord blood	blood
4	chr12:9100200-9101800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:9100200-9101800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr12:9100200-9103400	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr12:9100200-9103800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr12:9100200-9103800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:9100400-9102000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr12:9100400-9103600	Active TSS	HSMMtube	muscle
11	chr12:9100400-9103800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:9100400-9103800	Active TSS	Right Atrium	heart
13	chr12:9100400-9103800	Active TSS	K562	blood
14	chr12:9100400-9104000	Active TSS	GM12878-XiMat	blood
15	chr12:9100600-9101800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr12:9100600-9101800	Flanking Active TSS	Liver	Liver
17	chr12:9100600-9101800	Flanking Active TSS	HUVEC	blood vessel
18	chr12:9100600-9102000	Flanking Active TSS	Primary B cells from cord blood	blood
19	chr12:9100600-9102000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:9100600-9102000	Flanking Active TSS	Fetal Lung	lung
21	chr12:9100600-9103800	Active TSS	NHLF	lung
22	chr12:9100800-9101800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
23	chr12:9100800-9101800	Flanking Active TSS	Duodenum Mucosa	Duodenum
24	chr12:9100800-9101800	Flanking Active TSS	Fetal Brain Female	brain
25	chr12:9100800-9101800	Flanking Active TSS	Fetal Muscle Leg	muscle
26	chr12:9100800-9102000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:9100800-9102000	Flanking Active TSS	Osteobl	bone
28	chr12:9100800-9103400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:9100800-9103600	Active TSS	H1 Cell Line	embryonic stem cell
30	chr12:9101000-9101800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
31	chr12:9101000-9101800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr12:9101000-9101800	Flanking Active TSS	Brain Substantia Nigra	brain
33	chr12:9101000-9101800	Flanking Active TSS	Fetal Stomach	stomach
34	chr12:9101000-9101800	Flanking Active TSS	Rectal Smooth Muscle	rectum
35	chr12:9101000-9101800	Flanking Active TSS	Stomach Smooth Muscle	stomach
36	chr12:9101000-9102000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr12:9101000-9102000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
38	chr12:9101000-9102200	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr12:9101000-9102200	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr12:9101000-9102200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr12:9101000-9103400	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr12:9101000-9103400	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr12:9101000-9103600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:9101000-9103600	Active TSS	HUES48 Cell Line	embryonic stem cell
45	chr12:9101000-9103600	Active TSS	Fetal Intestine Small	intestine
46	chr12:9101000-9103600	Active TSS	Right Ventricle	heart
47	chr12:9101000-9103600	Active TSS	HSMM	muscle
48	chr12:9101000-9103800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr12:9101000-9103800	Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr12:9101000-9103800	Active TSS	Fetal Intestine Large	intestine

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