Variant report

Variant	rs1678970
Chromosome Location	chr12:122461928-122461929
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	MYC	chr12:122460877-122462337	K562	blood:	n/a	chr12:122461435-122461444 chr12:122461436-122461443 chr12:122461434-122461445 chr12:122461433-122461446 chr12:122461435-122461445
2	REST	chr12:122461646-122462090	A549	lung:	n/a	chr12:122461933-122461946
3	SIN3AK20	chr12:122460780-122462191	MCF-7	breast:	n/a	n/a
4	REST	chr12:122461765-122461957	HepG2	liver:	n/a	chr12:122461933-122461946
5	POLR2A	chr12:122460733-122461974	MCF10A-Er-Src	breast:	n/a	n/a
6	SIN3AK20	chr12:122461132-122462011	PANC-1	pancreas:	n/a	n/a
7	REST	chr12:122461617-122461992	SK-N-SH	brain:	n/a	chr12:122461933-122461946
8	MAX	chr12:122460795-122462062	HCT-116	colon:	n/a	chr12:122461435-122461444 chr12:122461436-122461443 chr12:122461434-122461445 chr12:122461433-122461446 chr12:122461435-122461445
9	POLR2A	chr12:122461465-122461961	SK-N-SH	brain:	n/a	n/a
10	MAX	chr12:122460387-122462455	HepG2	liver:	n/a	chr12:122461435-122461444 chr12:122460774-122460783 chr12:122461436-122461443 chr12:122461434-122461445 chr12:122461433-122461446 chr12:122461435-122461445
11	REST	chr12:122460931-122462082	H1-neurons	neurons:	n/a	chr12:122461530-122461548 chr12:122461933-122461946
12	HDAC2	chr12:122461004-122462448	HepG2	liver:	n/a	chr12:122462370-122462384 chr12:122462367-122462381 chr12:122462362-122462376 chr12:122462365-122462379 chr12:122462363-122462377 chr12:122462369-122462383
13	YY1	chr12:122460918-122461984	A549	lung:	n/a	chr12:122461637-122461647
14	MAX	chr12:122459688-122462184	A549	lung:	n/a	chr12:122461435-122461444 chr12:122460774-122460783 chr12:122461436-122461443 chr12:122461434-122461445 chr12:122461433-122461446 chr12:122461435-122461445
15	ELF1	chr12:122460581-122462215	GM12878	blood:	n/a	chr12:122461414-122461425
16	POLR2A	chr12:122459504-122462244	K562	blood:	n/a	n/a
17	POLR2A	chr12:122460980-122462373	HepG2	liver:	n/a	n/a
18	RELA	chr12:122461151-122462281	GM10847	blood:	n/a	n/a
19	ETS1	chr12:122461280-122462056	K562	blood:	n/a	n/a
20	GATA3	chr12:122461279-122462005	A549	lung:	n/a	chr12:122461502-122461510
21	TAF1	chr12:122461564-122461976	K562	blood:	n/a	n/a
22	POLR2A	chr12:122461634-122462096	K562	blood:	n/a	n/a
23	YY1	chr12:122461327-122461970	ECC-1	luminal epithelium:	n/a	chr12:122461637-122461647
24	MXI1	chr12:122461241-122462026	K562	blood:	n/a	n/a
25	MXI1	chr12:122458987-122462622	IMR90	lung:	n/a	n/a
26	REST	chr12:122461729-122462092	PANC-1	pancreas:	n/a	chr12:122461933-122461946
27	ZBTB7A	chr12:122461779-122462064	K562	blood:	n/a	n/a
28	SIN3AK20	chr12:122461146-122462090	K562	blood:	n/a	n/a
29	SIN3AK20	chr12:122461002-122462014	A549	lung:	n/a	n/a
30	RELA	chr12:122461309-122461964	GM19099	blood:	n/a	n/a
31	MAX	chr12:122460227-122462026	ECC-1	luminal epithelium:	n/a	chr12:122461435-122461444 chr12:122460774-122460783 chr12:122461436-122461443 chr12:122461434-122461445 chr12:122461433-122461446 chr12:122461435-122461445
32	SIN3A	chr12:122460344-122462087	H1-hESC	embryonic stem cell:	n/a	chr12:122461909-122461917 chr12:122461220-122461229
33	MAX	chr12:122460219-122462478	K562	blood:	n/a	chr12:122461435-122461444 chr12:122460774-122460783 chr12:122461436-122461443 chr12:122461434-122461445 chr12:122461433-122461446 chr12:122461435-122461445
34	TEAD4	chr12:122461165-122462024	K562	blood:	n/a	n/a
35	RELA	chr12:122461123-122462174	GM12891	blood:	n/a	n/a
36	YY1	chr12:122461223-122462103	SK-N-SH	brain:	n/a	chr12:122461637-122461647
37	YY1	chr12:122461286-122462149	K562	blood:	n/a	chr12:122461637-122461647
38	REST	chr12:122461745-122462046	K562	blood:	n/a	chr12:122461933-122461946
39	REST	chr12:122461695-122462088	MCF-7	breast:	n/a	chr12:122461933-122461946
40	UBTF	chr12:122459774-122462155	K562	blood:	n/a	n/a
41	TCF12	chr12:122460784-122462564	A549	lung:	n/a	chr12:122461929-122461936 chr12:122461930-122461940
42	E2F6	chr12:122461599-122461980	K562	blood:	n/a	n/a
43	ETS1	chr12:122461621-122462024	K562	blood:	n/a	n/a
44	MXI1	chr12:122461170-122462282	HepG2	liver:	n/a	n/a
45	SIN3AK20	chr12:122460992-122462073	MCF-7	breast:	n/a	n/a
46	REST	chr12:122461714-122461946	PFSK-1	brain:	n/a	chr12:122461933-122461946
47	CEBPB	chr12:122461297-122461976	HepG2	liver:	n/a	n/a
48	YY1	chr12:122461171-122461968	ECC-1	luminal epithelium:	n/a	chr12:122461637-122461647
49	HEY1	chr12:122460596-122461978	K562	blood:	n/a	n/a
50	YY1	chr12:122461303-122461938	SK-N-SH_RA	brain:	n/a	chr12:122461637-122461647

No.	Distal block	Cell Line	Cell type
1	chr12:122235921..122238772-chr12:122461316..122462876,2	K562	blood:
2	chr12:122459612..122462299-chr12:122516387..122519300,2	K562	blood:
3	chr12:122459811..122462052-chr12:122500619..122502679,2	K562	blood:
4	chr12:122230934..122233822-chr12:122459500..122463009,3	MCF-7	breast:
5	chr12:122237430..122243628-chr12:122458689..122463112,11	MCF-7	breast:
6	chr12:122356337..122361793-chr12:122458841..122462522,5	MCF-7	breast:
7	chr12:122325408..122328152-chr12:122461584..122463358,2	K562	blood:
8	chr12:122428522..122431508-chr12:122460147..122462626,2	MCF-7	breast:
9	chr12:122459975..122462130-chr12:122612185..122613777,2	MCF-7	breast:
10	chr12:122393562..122396353-chr12:122460972..122463920,2	K562	blood:
11	chr12:122369123..122373485-chr12:122458454..122462950,5	K562	blood:
12	chr12:122355313..122357386-chr12:122460176..122462387,2	K562	blood:
13	chr12:122325420..122328140-chr12:122460188..122462460,4	MCF-7	breast:
14	chr12:122236783..122240484-chr12:122457021..122461932,5	MCF-7	breast:
15	chr12:122459684..122462243-chr12:122749527..122751932,2	MCF-7	breast:
16	chr12:122461383..122462889-chr12:122756023..122758589,2	K562	blood:
17	chr12:122460064..122462817-chr12:122499395..122500991,2	MCF-7	breast:
18	chr12:122459405..122462233-chr12:122501246..122503627,3	MCF-7	breast:
19	chr12:122460432..122462517-chr12:122503179..122505981,2	MCF-7	breast:
20	chr12:122353381..122358597-chr12:122457924..122463718,11	MCF-7	breast:
21	chr12:122459539..122463256-chr12:122498402..122502892,4	MCF-7	breast:
22	chr12:122235276..122236948-chr12:122459921..122462305,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255856	TF binding region
ENSG00000212694	Chromatin interaction
ENSG00000175727	Chromatin interaction
ENSG00000139718	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000256950	Chromatin interaction
ENSG00000256546	Chromatin interaction
ENSG00000139719	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000272849	Chromatin interaction
ENSG00000256861	Chromatin interaction
ENSG00000139725	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs1169076	0.84[ASN][1000 genomes]
rs1169081	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1169083	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1169084	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1169086	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1169087	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1169091	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1179947	0.88[ASN][1000 genomes]
rs1184893	0.80[ASN][1000 genomes]
rs1814592	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2009257	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2018749	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2272133	0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55929316	0.94[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs59397548	0.80[AMR][1000 genomes]
rs830115	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs830121	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	esv34001	chr12:122298737-122521637	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	esv3338715	chr12:122457569-122462467	Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	esv3425442	chr12:122459394-122461942	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122459000-122462000	Active TSS	Fetal Kidney	kidney
2	chr12:122459200-122462000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr12:122459200-122462000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:122459200-122462000	Active TSS	Colon Smooth Muscle	Colon
5	chr12:122459200-122462000	Active TSS	Ovary	ovary
6	chr12:122459200-122462400	Active TSS	Aorta	Aorta
7	chr12:122459200-122462400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr12:122459400-122462000	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr12:122459400-122462000	Active TSS	Rectal Mucosa Donor 31	rectum
10	chr12:122459400-122462000	Active TSS	Rectal Smooth Muscle	rectum
11	chr12:122459400-122462000	Active TSS	HSMM	muscle
12	chr12:122459400-122462000	Active TSS	HSMMtube	muscle
13	chr12:122459600-122462200	Active TSS	Right Atrium	heart
14	chr12:122460600-122462000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
15	chr12:122460600-122462200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:122460800-122462000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
17	chr12:122460800-122462000	Flanking Active TSS	Colonic Mucosa	Colon
18	chr12:122460800-122462200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr12:122460800-122462200	Flanking Active TSS	Adipose Nuclei	Adipose
20	chr12:122460800-122462200	Flanking Active TSS	NH-A	brain
21	chr12:122460800-122462400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:122460800-122462400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr12:122460800-122462400	Flanking Active TSS	Fetal Muscle Trunk	muscle
24	chr12:122460800-122462400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr12:122460800-122462600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:122460800-122462600	Enhancers	Fetal Heart	heart
27	chr12:122460800-122463200	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr12:122461000-122462000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
29	chr12:122461000-122462000	Flanking Active TSS	HUVEC	blood vessel
30	chr12:122461000-122462200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr12:122461000-122462200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:122461000-122462200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:122461000-122462200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:122461000-122462400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr12:122461000-122462400	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr12:122461000-122462400	Flanking Active TSS	Stomach Smooth Muscle	stomach
37	chr12:122461000-122462400	Transcr. at gene 5' and 3'	Dnd41	blood
38	chr12:122461000-122462400	Flanking Active TSS	K562	blood
39	chr12:122461000-122462400	Flanking Active TSS	NHLF	lung
40	chr12:122461000-122462600	Flanking Active TSS	Primary B cells from peripheral blood	blood
41	chr12:122461200-122462000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr12:122461200-122462200	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:122461200-122462200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:122461200-122462200	Flanking Active TSS	Liver	Liver
45	chr12:122461200-122462200	Flanking Active TSS	Brain Anterior Caudate	brain
46	chr12:122461200-122462200	Flanking Active TSS	Fetal Intestine Large	intestine
47	chr12:122461200-122462200	Flanking Active TSS	Fetal Intestine Small	intestine
48	chr12:122461200-122462200	Flanking Active TSS	A549	lung
49	chr12:122461200-122462400	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:122461200-122462400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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