Variant report

Variant	rs7954584
Chromosome Location	chr12:122461566-122461567
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	YY1	chr12:122461355-122461887	SK-N-SH_RA	brain:	n/a	chr12:122461637-122461647
3	SIN3AK20	chr12:122460780-122462191	MCF-7	breast:	n/a	n/a
4	USF1	chr12:122461164-122461676	A549	lung:	n/a	n/a
5	POLR2A	chr12:122460733-122461974	MCF10A-Er-Src	breast:	n/a	n/a
6	MYBL2	chr12:122461113-122461855	HepG2	liver:	n/a	n/a
7	POLR2A	chr12:122461233-122461566	HUVEC	blood vessel:	n/a	n/a
8	POLR2A	chr12:122460988-122461710	HUVEC	blood vessel:	n/a	n/a
9	FOXA1	chr12:122461119-122461665	T-47D	breast:	n/a	n/a
10	SIN3AK20	chr12:122461132-122462011	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr12:122461388-122461591	HUVEC	blood vessel:	n/a	n/a
12	MAX	chr12:122460795-122462062	HCT-116	colon:	n/a	chr12:122461435-122461444 chr12:122461436-122461443 chr12:122461434-122461445 chr12:122461433-122461446 chr12:122461435-122461445
13	RAD21	chr12:122461539-122461890	SK-N-SH_RA	brain:	n/a	n/a
14	FOXM1	chr12:122461555-122461903	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:122461465-122461961	SK-N-SH	brain:	n/a	n/a
16	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
17	REST	chr12:122460931-122462082	H1-neurons	neurons:	n/a	chr12:122461530-122461548 chr12:122461933-122461946
18	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
19	USF1	chr12:122461249-122461716	ECC-1	luminal epithelium:	n/a	n/a
20	SIN3A	chr12:122461415-122461744	GM12878	blood:	n/a	n/a
21	YY1	chr12:122460918-122461984	A549	lung:	n/a	chr12:122461637-122461647
22	E2F6	chr12:122461324-122461582	K562	blood:	n/a	n/a
23	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
24	ELF1	chr12:122460581-122462215	GM12878	blood:	n/a	chr12:122461414-122461425
25	POLR2A	chr12:122459504-122462244	K562	blood:	n/a	n/a
26	POLR2A	chr12:122460980-122462373	HepG2	liver:	n/a	n/a
27	RELA	chr12:122461151-122462281	GM10847	blood:	n/a	n/a
28	ETS1	chr12:122461280-122462056	K562	blood:	n/a	n/a
29	USF1	chr12:122461286-122461574	HepG2	liver:	n/a	n/a
30	FOXA1	chr12:122461140-122461586	HepG2	liver:	n/a	n/a
31	SIN3AK20	chr12:122461259-122461770	PFSK-1	brain:	n/a	n/a
32	GATA3	chr12:122461279-122462005	A549	lung:	n/a	chr12:122461502-122461510
33	MYC	chr12:122461313-122461625	K562	blood:	n/a	chr12:122461435-122461444 chr12:122461436-122461443 chr12:122461434-122461445 chr12:122461433-122461446 chr12:122461435-122461445
34	TAF1	chr12:122461564-122461976	K562	blood:	n/a	n/a
35	YY1	chr12:122461327-122461970	ECC-1	luminal epithelium:	n/a	chr12:122461637-122461647
36	MXI1	chr12:122461241-122462026	K562	blood:	n/a	n/a
37	MXI1	chr12:122458987-122462622	IMR90	lung:	n/a	n/a
38	BCL3	chr12:122461280-122461740	A549	lung:	n/a	chr12:122461705-122461714
39	FOXA1	chr12:122460704-122461692	HepG2	liver:	n/a	n/a
40	MAX	chr12:122461226-122461764	GM12878	blood:	n/a	chr12:122461435-122461444 chr12:122461436-122461443 chr12:122461434-122461445 chr12:122461433-122461446 chr12:122461435-122461445
41	BACH1	chr12:122461369-122461569	H1-hESC	embryonic stem cell:	n/a	n/a
42	SIN3AK20	chr12:122461146-122462090	K562	blood:	n/a	n/a
43	USF1	chr12:122461046-122461821	HCT-116	colon:	n/a	n/a
44	SIN3AK20	chr12:122461002-122462014	A549	lung:	n/a	n/a
45	RELA	chr12:122461309-122461964	GM19099	blood:	n/a	n/a
46	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
47	POLR2A	chr12:122461398-122461833	H1-neurons	neurons:	n/a	n/a
48	E2F6	chr12:122460787-122461675	H1-hESC	embryonic stem cell:	n/a	chr12:122460861-122460871
49	SIN3A	chr12:122460344-122462087	H1-hESC	embryonic stem cell:	n/a	chr12:122461909-122461917 chr12:122461220-122461229
50	USF2	chr12:122461271-122461595	Hela-S3	cervix:	n/a	n/a

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	chr12:122459459..122461695-chr12:122710698..122713171,3	MCF-7	breast:
5	chr12:122230934..122233822-chr12:122459500..122463009,3	MCF-7	breast:
6	chr12:122237430..122243628-chr12:122458689..122463112,11	MCF-7	breast:
7	chr12:122356337..122361793-chr12:122458841..122462522,5	MCF-7	breast:
8	chr12:122370271..122373728-chr12:122458243..122461695,4	K562	blood:
9	chr12:122295977..122297667-chr12:122459919..122461653,2	K562	blood:
10	chr12:122428522..122431508-chr12:122460147..122462626,2	MCF-7	breast:
11	chr12:122458897..122461646-chr12:122516392..122519046,3	MCF-7	breast:
12	chr12:122459975..122462130-chr12:122612185..122613777,2	MCF-7	breast:
13	chr12:122393562..122396353-chr12:122460972..122463920,2	K562	blood:
14	chr12:122369123..122373485-chr12:122458454..122462950,5	K562	blood:
15	chr12:122355313..122357386-chr12:122460176..122462387,2	K562	blood:
16	chr12:122325420..122328140-chr12:122460188..122462460,4	MCF-7	breast:
17	chr12:122236783..122240484-chr12:122457021..122461932,5	MCF-7	breast:
18	chr12:122459684..122462243-chr12:122749527..122751932,2	MCF-7	breast:
19	chr12:122457987..122461924-chr12:122515396..122519074,6	MCF-7	breast:
20	chr12:122461383..122462889-chr12:122756023..122758589,2	K562	blood:
21	chr12:122460064..122462817-chr12:122499395..122500991,2	MCF-7	breast:
22	chr12:122459405..122462233-chr12:122501246..122503627,3	MCF-7	breast:
23	chr12:122460432..122462517-chr12:122503179..122505981,2	MCF-7	breast:
24	chr12:122353381..122358597-chr12:122457924..122463718,11	MCF-7	breast:
25	chr12:122459539..122463256-chr12:122498402..122502892,4	MCF-7	breast:
26	chr12:122235276..122236948-chr12:122459921..122462305,2	MCF-7	breast:
27	chr12:122437989..122441020-chr12:122459413..122461657,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000255856	TF binding region
ENSG00000212694	Chromatin interaction
ENSG00000256546	Chromatin interaction
ENSG00000256950	Chromatin interaction
ENSG00000272849	Chromatin interaction
ENSG00000175727	Chromatin interaction
ENSG00000158104	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000110801	Chromatin interaction
ENSG00000184047	Chromatin interaction
ENSG00000158023	Chromatin interaction
ENSG00000139719	Chromatin interaction
ENSG00000256861	Chromatin interaction
ENSG00000139718	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10840631	0.85[MEX][hapmap]
rs10840632	0.90[MEX][hapmap]
rs10840635	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10840640	0.83[EUR][1000 genomes]
rs10840641	0.83[EUR][1000 genomes]
rs11043249	0.81[JPT][hapmap]
rs11043252	0.81[JPT][hapmap]
rs11043265	0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs11043271	0.90[MEX][hapmap]
rs11043276	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11043288	0.82[CEU][hapmap];0.95[MEX][hapmap];0.85[TSI][hapmap]
rs12827036	0.90[MEX][hapmap]
rs1523261	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1720033	0.80[MEX][hapmap]
rs1720037	0.80[MEX][hapmap]
rs3847694	0.85[MEX][hapmap]
rs6486784	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs6486785	0.81[JPT][hapmap]
rs7132055	0.80[MEX][hapmap]
rs7139277	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7298520	0.81[JPT][hapmap]
rs7300379	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7314989	0.89[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]

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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7954584	BCL7A	cis	Muscle Skeletal	GTEx
rs7954584	WDR66	cis	cerebellum	SCAN
rs7954584	FBXO21	cis	cerebellum	SCAN
rs7954584	CCDC60	cis	cerebellum	SCAN
rs7954584	FAM101A	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122458800-122461800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:122459000-122461800	Active TSS	Psoas Muscle	Psoas
3	chr12:122459000-122461800	Active TSS	Thymus	Thymus
4	chr12:122459000-122462000	Active TSS	Fetal Kidney	kidney
5	chr12:122459200-122461600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr12:122459200-122461600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:122459200-122461600	Active TSS	Lung	lung
8	chr12:122459200-122461600	Active TSS	Right Ventricle	heart
9	chr12:122459200-122461800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:122459200-122461800	Active TSS	Fetal Brain Female	brain
11	chr12:122459200-122462000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:122459200-122462000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:122459200-122462000	Active TSS	Colon Smooth Muscle	Colon
14	chr12:122459200-122462000	Active TSS	Ovary	ovary
15	chr12:122459200-122462400	Active TSS	Aorta	Aorta
16	chr12:122459200-122462400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr12:122459400-122461600	Active TSS	Primary T cells from cord blood	blood
18	chr12:122459400-122461600	Active TSS	Muscle Satellite Cultured Cells	--
19	chr12:122459400-122461600	Active TSS	Brain Angular Gyrus	brain
20	chr12:122459400-122461600	Active TSS	Gastric	stomach
21	chr12:122459400-122461800	Active TSS	H9 Cell Line	embryonic stem cell
22	chr12:122459400-122461800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:122459400-122461800	Active TSS	Brain Cingulate Gyrus	brain
24	chr12:122459400-122461800	Active TSS	Brain Inferior Temporal Lobe	brain
25	chr12:122459400-122461800	Active TSS	Brain Substantia Nigra	brain
26	chr12:122459400-122461800	Active TSS	Left Ventricle	heart
27	chr12:122459400-122461800	Active TSS	Pancreas	Pancrea
28	chr12:122459400-122462000	Active TSS	Breast Myoepithelial Primary Cells	Breast
29	chr12:122459400-122462000	Active TSS	Rectal Mucosa Donor 31	rectum
30	chr12:122459400-122462000	Active TSS	Rectal Smooth Muscle	rectum
31	chr12:122459400-122462000	Active TSS	HSMM	muscle
32	chr12:122459400-122462000	Active TSS	HSMMtube	muscle
33	chr12:122459600-122461600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:122459600-122461800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:122459600-122461800	Active TSS	Brain Germinal Matrix	brain
36	chr12:122459600-122462200	Active TSS	Right Atrium	heart
37	chr12:122460600-122461600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
38	chr12:122460600-122461800	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr12:122460600-122462000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
40	chr12:122460600-122462200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:122460800-122461600	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
42	chr12:122460800-122461600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:122460800-122461600	Active TSS	Fetal Brain Male	brain
44	chr12:122460800-122461600	Flanking Active TSS	Placenta	Placenta
45	chr12:122460800-122461800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr12:122460800-122461800	Active TSS	Stomach Mucosa	stomach
47	chr12:122460800-122461800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
48	chr12:122460800-122462000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
49	chr12:122460800-122462000	Flanking Active TSS	Colonic Mucosa	Colon
50	chr12:122460800-122462200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links