Variant report

Variant	rs12175856
Chromosome Location	chr6:144471575-144471576
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	POLR2A	chr6:144471065-144472989	GM18526	blood:	n/a	n/a
2	MYC	chr6:144471287-144471855	NB4	blood:	n/a	n/a
3	EP300	chr6:144471481-144471824	H1-hESC	embryonic stem cell:	n/a	chr6:144471714-144471730 chr6:144471643-144471652 chr6:144471661-144471677 chr6:144471565-144471581 chr6:144471646-144471662 chr6:144471641-144471650
4	YY1	chr6:144471446-144471796	K562	blood:	n/a	chr6:144471644-144471653 chr6:144471660-144471674 chr6:144471658-144471669 chr6:144471555-144471566 chr6:144471666-144471675 chr6:144471663-144471672 chr6:144471660-144471669 chr6:144471720-144471734
5	TAF1	chr6:144471164-144471799	GM12878	blood:	n/a	n/a
6	TCF12	chr6:144471209-144471781	GM12878	blood:	n/a	n/a
7	FOXM1	chr6:144470920-144471745	GM12878	blood:	n/a	n/a
8	CHD2	chr6:144470993-144471833	GM12878	blood:	n/a	chr6:144471204-144471214 chr6:144471426-144471436
9	POLR2A	chr6:144471061-144473373	GM12878	blood:	n/a	n/a
10	MAZ	chr6:144470954-144471879	IMR90	lung:	n/a	n/a
11	MAX	chr6:144471185-144472907	Hela-S3	cervix:	n/a	chr6:144472552-144472561 chr6:144472770-144472780
12	TAF1	chr6:144471334-144471896	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr6:144471120-144471701	GM12878	blood:	n/a	n/a
14	BCLAF1	chr6:144471058-144471910	GM12878	blood:	n/a	chr6:144471297-144471310 chr6:144471868-144471877 chr6:144471350-144471359 chr6:144471727-144471740 chr6:144471717-144471730 chr6:144471664-144471673 chr6:144471563-144471572 chr6:144471627-144471636 chr6:144471557-144471570 chr6:144471848-144471857 chr6:144471329-144471342 chr6:144471661-144471670
15	MAX	chr6:144471328-144471643	K562	blood:	n/a	n/a
16	RELA	chr6:144470940-144471713	GM12892	blood:	n/a	n/a
17	SIN3AK20	chr6:144471191-144471854	H1-hESC	embryonic stem cell:	n/a	n/a
18	RELA	chr6:144470832-144471767	GM10847	blood:	n/a	n/a
19	MYC	chr6:144471105-144471621	MCF-7	breast:	n/a	n/a
20	POU2F2	chr6:144471097-144471879	GM12891	blood:	n/a	n/a
21	POLR2A	chr6:144471308-144471842	Hela-S3	cervix:	n/a	n/a
22	BHLHE40	chr6:144470962-144471751	GM12878	blood:	n/a	chr6:144471557-144471573 chr6:144471709-144471725 chr6:144471495-144471511
23	MAX	chr6:144470989-144471704	H1-hESC	embryonic stem cell:	n/a	n/a
24	ZBTB7A	chr6:144471345-144472047	K562	blood:	n/a	chr6:144471609-144471620
25	POLR2A	chr6:144471092-144472033	GM12878	blood:	n/a	n/a
26	POLR2A	chr6:144470893-144472015	GM12892	blood:	n/a	n/a
27	SP1	chr6:144471125-144471693	GM12878	blood:	n/a	chr6:144471587-144471599 chr6:144471589-144471598 chr6:144471587-144471599 chr6:144471589-144471598 chr6:144471261-144471271 chr6:144471584-144471597 chr6:144471261-144471271 chr6:144471588-144471597
28	YY1	chr6:144471375-144471670	HCT-116	colon:	n/a	chr6:144471644-144471653 chr6:144471435-144471449 chr6:144471658-144471669 chr6:144471555-144471566 chr6:144471660-144471669
29	FOXP2	chr6:144471349-144471736	PFSK-1	brain:	n/a	n/a
30	PML	chr6:144471515-144471822	GM12878	blood:	n/a	n/a
31	POLR2A	chr6:144471074-144472027	GM12878	blood:	n/a	n/a
32	RFX5	chr6:144471338-144471782	Hela-S3	cervix:	n/a	n/a
33	MXI1	chr6:144471297-144471748	HepG2	liver:	n/a	n/a
34	TCF12	chr6:144471185-144471916	ECC-1	luminal epithelium:	n/a	n/a
35	RELA	chr6:144470986-144471840	GM19099	blood:	n/a	n/a
36	E2F6	chr6:144471365-144471646	K562	blood:	n/a	chr6:144471592-144471602 chr6:144471559-144471569 chr6:144471530-144471542 chr6:144471531-144471542
37	JUND	chr6:144471331-144471667	K562	blood:	n/a	n/a
38	POLR2A	chr6:144471088-144471943	HUVEC	blood vessel:	n/a	n/a
39	RCOR1	chr6:144471019-144473008	GM12878	blood:	n/a	n/a
40	POU2F2	chr6:144471064-144471887	GM12878	blood:	n/a	n/a
41	MXI1	chr6:144471032-144473759	GM12878	blood:	n/a	n/a
42	YY1	chr6:144471171-144471831	GM12891	blood:	n/a	chr6:144471644-144471653 chr6:144471435-144471449 chr6:144471660-144471674 chr6:144471658-144471669 chr6:144471555-144471566 chr6:144471666-144471675 chr6:144471663-144471672 chr6:144471660-144471669 chr6:144471249-144471263 chr6:144471720-144471734
43	CCNT2	chr6:144471222-144471845	K562	blood:	n/a	n/a
44	EP300	chr6:144471220-144471607	GM12878	blood:	n/a	chr6:144471565-144471581
45	HA-E2F1	chr6:144470627-144471876	MCF-7	breast:	n/a	chr6:144471530-144471541 chr6:144471592-144471602 chr6:144471559-144471569 chr6:144471530-144471542 chr6:144471666-144471675
46	POLR2A	chr6:144471193-144471973	Raji	blood:	n/a	n/a
47	CTCF	chr6:144471217-144472625	GM12878	blood:	n/a	chr6:144471708-144471721 chr6:144471787-144471800
48	MAX	chr6:144470822-144471726	MCF-7	breast:	n/a	n/a
49	TAF1	chr6:144471532-144471780	H1-hESC	embryonic stem cell:	n/a	n/a
50	POLR2A	chr6:144471414-144471888	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:144471564-144471614	HRPEpiC	eye:	n/a
2	chr6:144471564-144471614	NH-A	brain:	n/a
3	chr6:144471564-144471614	MCF-7	breast:	n/a
4	chr6:144471564-144471614	ProgFib	skin:	n/a
5	chr6:144471564-144471614	HNPCEpiC	eye:	n/a
6	chr6:144471564-144471614	ECC-1	luminal epithelium:	n/a
7	chr6:144471564-144471614	HPAEpiC	pulmonary alveolar:	n/a
8	chr6:144471564-144471614	CMK	blood:	n/a
9	chr6:144471564-144471614	BE2_C	brain:	n/a
10	chr6:144471564-144471614	NT2-D1	testis:	n/a
11	chr6:144471564-144471614	U87	brain:	n/a
12	chr6:144471564-144471614	Hepatocyte	liver:	n/a
13	chr6:144471564-144471614	ovcar-3	ovarian:	n/a
14	chr6:144471564-144471614	IMR90	lung:	fetal
15	chr6:144471564-144471614	HRCEpiC	kidney:	n/a
16	chr6:144471564-144471614	HEK293	kidney:	embryo
17	chr6:144471564-144471614	Hela-S3	cervix:	n/a
18	chr6:144471564-144471614	NHDF-neo	bronchial:	n/a
19	chr6:144471564-144471614	AG09319	gingival:	n/a
20	chr6:144471564-144471614	PFSK-1	brain:	n/a
21	chr6:144471564-144471614	Caco-2	colon:	n/a
22	chr6:144471564-144471614	NB4	blood:	n/a
23	chr6:144471564-144471614	GM12892	blood:	n/a
24	chr6:144471564-144471614	HIPEpiC	eye:	n/a
25	chr6:144471564-144471614	GM19239	blood:	n/a
26	chr6:144471564-144471614	HRE	kidney:	n/a
27	chr6:144471564-144471614	RPTEC	kidney:	n/a
28	chr6:144471564-144471614	HepG2	liver:	n/a
29	chr6:144471564-144471614	HL-60	blood:	n/a
30	chr6:144471564-144471614	SAEC	small airway:	n/a
31	chr6:144471564-144471614	K562	blood:	n/a
32	chr6:144471564-144471614	HCPEpiC	choroid plexus:	n/a
33	chr6:144471564-144471614	HCF	heart:	n/a
34	chr6:144471564-144471614	SK-N-MC	brain:	n/a
35	chr6:144471564-144471614	HCM	heart:	n/a
36	chr6:144471564-144471614	LNCaP	prostate:	n/a
37	chr6:144471564-144471614	A549	lung:	n/a
38	chr6:144471564-144471614	SK-N-SH	brain:	n/a
39	chr6:144471564-144471614	AG04450	lung:	fetal
40	chr6:144471564-144471614	Jurkat	blood:	n/a
41	chr6:144471564-144471614	MCF10A-Er-Src	breast:	n/a
42	chr6:144471564-144471614	PrEC	prostate:	n/a
43	chr6:144471564-144471614	NHBE	bronchial:	n/a
44	chr6:144471564-144471614	SKMC	muscle:	n/a
45	chr6:144471564-144471614	GM12878	blood:	n/a
46	chr6:144471564-144471614	HMEC	breast:	n/a
47	chr6:144471564-144471614	SK-N-SH_RA	brain:	n/a
48	chr6:144471564-144471614	GM06990	blood:	n/a
49	chr6:144471564-144471614	HCT-116	colon:	n/a
50	chr6:144471564-144471614	PANC-1	pancreas:	n/a

Variant related genes	Relation type
STX11	TF binding region
STX11	CpG island

Extended variants
information (count: 6 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12207102	1.00[YRI][hapmap]
rs1983773	1.00[YRI][hapmap]
rs2328564	1.00[YRI][hapmap]
rs9390157	1.00[YRI][hapmap]
rs9403540	1.00[LWK][hapmap]

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	nsv1024333	chr6:144468065-144502824	Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12175856	C6orf94	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144470400-144473200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:144470600-144472200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
3	chr6:144470600-144472200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr6:144470600-144472400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr6:144470600-144472800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:144470600-144473000	Active TSS	Right Ventricle	heart
7	chr6:144470800-144471600	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:144470800-144471600	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr6:144470800-144471600	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr6:144470800-144471600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr6:144470800-144472000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
12	chr6:144470800-144472000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:144470800-144472000	Active TSS	Brain Angular Gyrus	brain
14	chr6:144470800-144472000	Active TSS	Brain Inferior Temporal Lobe	brain
15	chr6:144470800-144472000	Active TSS	NH-A	brain
16	chr6:144470800-144472200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr6:144470800-144472200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:144470800-144472200	Active TSS	Colon Smooth Muscle	Colon
19	chr6:144470800-144472200	Bivalent/Poised TSS	Fetal Brain Female	brain
20	chr6:144470800-144472200	Active TSS	Rectal Smooth Muscle	rectum
21	chr6:144470800-144472200	Active TSS	NHLF	lung
22	chr6:144470800-144472400	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:144470800-144472400	Active TSS	Primary T cells from cord blood	blood
24	chr6:144470800-144472400	Active TSS	Brain Hippocampus Middle	brain
25	chr6:144470800-144472400	Active TSS	Duodenum Smooth Muscle	Duodenum
26	chr6:144470800-144472400	Active TSS	A549	lung
27	chr6:144470800-144472600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
28	chr6:144470800-144472600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
29	chr6:144470800-144472600	Active TSS	Primary T helper naive cells from peripheral blood	blood
30	chr6:144470800-144472800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:144470800-144472800	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr6:144470800-144473000	Active TSS	Right Atrium	heart
33	chr6:144470800-144473400	Bivalent/Poised TSS	Psoas Muscle	Psoas
34	chr6:144471000-144471600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:144471000-144471600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
36	chr6:144471000-144471600	Flanking Active TSS	Liver	Liver
37	chr6:144471000-144471600	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
38	chr6:144471000-144471600	Flanking Active TSS	Thymus	Thymus
39	chr6:144471000-144471600	Flanking Bivalent TSS/Enh	Dnd41	blood
40	chr6:144471000-144471800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr6:144471000-144472000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:144471000-144472200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr6:144471000-144472200	Active TSS	Brain Anterior Caudate	brain
44	chr6:144471000-144472200	Bivalent/Poised TSS	Brain Germinal Matrix	brain
45	chr6:144471000-144472200	Active TSS	Brain Substantia Nigra	brain
46	chr6:144471000-144472200	Active TSS	Rectal Mucosa Donor 31	rectum
47	chr6:144471000-144472200	Active TSS	HSMM	muscle
48	chr6:144471000-144472200	Active TSS	HSMMtube	muscle
49	chr6:144471000-144472400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr6:144471000-144472400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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