Variant report

Variant	rs28655666
Chromosome Location	chr12:122186317-122186318
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	MAX	chr12:122186082-122187393	MCF-7	breast:	n/a	chr12:122186697-122186708
2	MAX	chr12:122186077-122187479	A549	lung:	n/a	chr12:122186697-122186708
3	POLR2A	chr12:122185684-122186695	A549	lung:	n/a	n/a
4	SP1	chr12:122186109-122187332	A549	lung:	n/a	chr12:122187020-122187034
5	MAZ	chr12:122186100-122187497	IMR90	lung:	n/a	chr12:122186697-122186708
6	CREB1	chr12:122186068-122187186	A549	lung:	n/a	n/a
7	CBX3	chr12:122186272-122187455	K562	blood:	n/a	chr12:122187076-122187087
8	JUN	chr12:122186101-122187534	K562	blood:	n/a	chr12:122186877-122186886 chr12:122186693-122186702 chr12:122186873-122186886
9	JUND	chr12:122186218-122187280	A549	lung:	n/a	chr12:122186877-122186886 chr12:122186693-122186702
10	GATA3	chr12:122186226-122187175	MCF-7	breast:	n/a	chr12:122186477-122186484 chr12:122186475-122186485 chr12:122186475-122186484
11	E2F6	chr12:122186094-122187204	A549	lung:	n/a	chr12:122186694-122186703
12	TEAD4	chr12:122186224-122187321	K562	blood:	n/a	chr12:122186496-122186505
13	POLR2A	chr12:122185723-122186718	A549	lung:	n/a	n/a
14	FOXM1	chr12:122186157-122187333	MCF-7	breast:	n/a	n/a
15	CREB1	chr12:122186119-122187271	K562	blood:	n/a	n/a
16	EP300	chr12:122186097-122187324	A549	lung:	n/a	n/a
17	MAX	chr12:122186091-122187400	A549	lung:	n/a	chr12:122186697-122186708
18	GATA3	chr12:122186308-122186911	T-47D	breast:	n/a	chr12:122186477-122186484 chr12:122186475-122186485 chr12:122186475-122186484
19	MAX	chr12:122186169-122187024	A549	lung:	n/a	chr12:122186697-122186708
20	NR3C1	chr12:122185755-122187151	A549	lung:	n/a	chr12:122186880-122186906 chr12:122186593-122186600 chr12:122187002-122187011 chr12:122186622-122186631
21	NR3C1	chr12:122185701-122187286	A549	lung:	n/a	chr12:122186880-122186906 chr12:122186593-122186600 chr12:122187002-122187011 chr12:122186622-122186631 chr12:122187227-122187240
22	TEAD4	chr12:122186257-122187297	A549	lung:	n/a	chr12:122186496-122186505
23	NR3C1	chr12:122185670-122187292	A549	lung:	n/a	chr12:122186880-122186906 chr12:122186593-122186600 chr12:122187002-122187011 chr12:122186622-122186631 chr12:122187227-122187240
24	E2F6	chr12:122186223-122187110	K562	blood:	n/a	chr12:122186694-122186703
25	NR2F2	chr12:122186193-122187273	MCF-7	breast:	n/a	n/a
26	HDAC2	chr12:122186163-122187335	MCF-7	breast:	n/a	chr12:122186476-122186485
27	REST	chr12:122186265-122187020	A549	lung:	n/a	n/a
28	FOSL2	chr12:122186178-122187397	A549	lung:	n/a	chr12:122186877-122186886 chr12:122186693-122186702
29	BCL3	chr12:122186167-122187242	A549	lung:	n/a	n/a
30	REST	chr12:122186275-122186614	K562	blood:	n/a	n/a
31	BCL3	chr12:122186184-122187268	A549	lung:	n/a	n/a
32	YY1	chr12:122186264-122186703	A549	lung:	n/a	n/a
33	ELF1	chr12:122186160-122187269	MCF-7	breast:	n/a	chr12:122186675-122186687
34	RCOR1	chr12:122186306-122187246	K562	blood:	n/a	n/a
35	GATA3	chr12:122186136-122187468	A549	lung:	n/a	chr12:122186477-122186484 chr12:122186475-122186485 chr12:122186475-122186484
36	SIN3AK20	chr12:122186231-122187338	MCF-7	breast:	n/a	n/a
37	EP300	chr12:122186260-122187296	MCF-7	breast:	n/a	n/a
38	SP1	chr12:122185975-122187476	A549	lung:	n/a	chr12:122187020-122187034
39	SIN3AK20	chr12:122186267-122187149	A549	lung:	n/a	n/a
40	REST	chr12:122186117-122187376	A549	lung:	n/a	chr12:122187159-122187177
41	ATF3	chr12:122186269-122187325	A549	lung:	n/a	n/a
42	EP300	chr12:122186132-122187436	A549	lung:	n/a	n/a
43	CTCF	chr12:122186280-122186430	HRE	kidney:	n/a	n/a
44	TCF12	chr12:122186211-122187126	A549	lung:	n/a	chr12:122186600-122186607
45	GATA3	chr12:122186180-122187365	MCF-7	breast:	n/a	chr12:122186477-122186484 chr12:122186475-122186485 chr12:122186475-122186484
46	TEAD4	chr12:122186292-122187157	K562	blood:	n/a	chr12:122186496-122186505
47	TCF7L2	chr12:122186238-122186891	PANC-1	pancreas:	n/a	n/a
48	ETS1	chr12:122186105-122187176	A549	lung:	n/a	n/a
49	YY1	chr12:122186097-122187059	A549	lung:	n/a	n/a
50	TCF12	chr12:122186051-122187448	A549	lung:	n/a	chr12:122186600-122186607

No.	Distal block	Cell Line	Cell type
1	chr12:122149421..122152814-chr12:122185119..122186671,3	MCF-7	breast:
2	chr12:122184924..122187179-chr12:122189642..122193871,5	K562	blood:
3	chr12:122180307..122182295-chr12:122185324..122187863,3	K562	blood:
4	chr12:122185135..122187179-chr12:122190114..122193871,4	K562	blood:
5	chr12:122184835..122196012-chr12:122235281..122245445,27	MCF-7	breast:
6	chr12:122181102..122183945-chr12:122184844..122187780,3	MCF-7	breast:
7	chr12:122133742..122136740-chr12:122185481..122187047,2	MCF-7	breast:
8	chr12:121836861..121838700-chr12:122185043..122186944,2	K562	blood:
9	chr12:122148459..122151159-chr12:122185562..122188129,3	K562	blood:
10	chr12:122147215..122155218-chr12:122185094..122190846,22	MCF-7	breast:
11	chr12:122181727..122184365-chr12:122185006..122187114,3	MCF-7	breast:
12	chr12:122180307..122183056-chr12:122185275..122189745,5	K562	blood:
13	chr12:122185267..122187971-chr12:122239677..122241444,2	MCF-7	breast:
14	chr12:122185243..122188214-chr12:122238983..122240823,2	K562	blood:
15	chr12:122184667..122189513-chr12:122211148..122219682,10	MCF-7	breast:

Variant related genes	Relation type
TMEM120B	TF binding region
ENSG00000212694	Chromatin interaction
ENSG00000089053	Chromatin interaction
ENSG00000188735	Chromatin interaction
ENSG00000272849	Chromatin interaction
ENSG00000139718	Chromatin interaction
ENSG00000139725	Chromatin interaction
ENSG00000170633	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs10840615	0.88[EUR][1000 genomes]
rs28651018	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv1040169	chr12:122096825-122209555	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv899566	chr12:122167095-122265106	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
4	esv3500918	chr12:122183269-122188067	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
5	esv3495976	chr12:122184069-122186867	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
6	esv2625237	chr12:122184959-122186755	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv560471	chr12:122185258-122186317	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
8	nsv560472	chr12:122185258-122190385	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	nsv560478	chr12:122185309-122186317	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
10	nsv560488	chr12:122185616-122186317	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
11	nsv560489	chr12:122185616-122190385	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28655666	TMEM120B,RHOF	cis	cerebellar cortex	BrainEAC

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122152000-122188000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:122152200-122186400	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:122152200-122188000	Weak transcription	Brain Germinal Matrix	brain
4	chr12:122152200-122188000	Weak transcription	Dnd41	blood
5	chr12:122152200-122191600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:122152200-122191600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:122152200-122200200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr12:122152400-122188000	Weak transcription	Stomach Smooth Muscle	stomach
9	chr12:122154200-122200400	Weak transcription	Psoas Muscle	Psoas
10	chr12:122155200-122186400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr12:122158800-122186400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr12:122159200-122186400	Weak transcription	HSMM	muscle
13	chr12:122159400-122194800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr12:122163600-122186600	Weak transcription	HSMMtube	muscle
15	chr12:122163600-122188000	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr12:122163600-122188200	Weak transcription	Brain Anterior Caudate	brain
17	chr12:122164800-122188200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr12:122166800-122186400	Weak transcription	Colon Smooth Muscle	Colon
19	chr12:122167200-122186400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr12:122174200-122191800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr12:122176600-122186400	Weak transcription	Hela-S3	cervix
22	chr12:122176600-122187200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:122179800-122211000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr12:122180200-122191400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr12:122181200-122186400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr12:122181200-122186600	Weak transcription	Aorta	Aorta
27	chr12:122181200-122188200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr12:122181800-122186400	Weak transcription	Brain Angular Gyrus	brain
29	chr12:122182400-122186400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:122182600-122186600	Weak transcription	Primary T cells from cord blood	blood
31	chr12:122183000-122186800	Weak transcription	NHEK	skin
32	chr12:122183200-122186400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:122183200-122186400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:122183200-122188000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr12:122183200-122188600	Weak transcription	GM12878-XiMat	blood
36	chr12:122183800-122224400	Weak transcription	Small Intestine	intestine
37	chr12:122184800-122186400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:122184800-122188400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr12:122184800-122191600	Weak transcription	Brain Substantia Nigra	brain
40	chr12:122184800-122208000	Weak transcription	Colonic Mucosa	Colon
41	chr12:122185000-122187200	Weak transcription	Brain Hippocampus Middle	brain
42	chr12:122185000-122191400	Weak transcription	Primary B cells from peripheral blood	blood
43	chr12:122185400-122188000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr12:122185800-122188600	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr12:122186000-122187000	Genic enhancers	Right Ventricle	heart
46	chr12:122186000-122187600	Enhancers	Fetal Thymus	thymus
47	chr12:122186200-122186400	Genic enhancers	H1 Cell Line	embryonic stem cell
48	chr12:122186200-122186400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr12:122186200-122186400	Genic enhancers	HUES48 Cell Line	embryonic stem cell
50	chr12:122186200-122186400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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