Variant report

Variant	rs12422405
Chromosome Location	chr12:83081182-83081183
allele	A/C
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	chr12:83079327-83081865	A549	lung:	n/a	chr12:83081461-83081471
2	POLR2A	chr12:83079620-83081222	MCF-7	breast:	n/a	n/a
3	POLR2A	chr12:83080069-83081879	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr12:83079100-83082637	A549	lung:	n/a	chr12:83079640-83079656 chr12:83081477-83081490 chr12:83079639-83079657 chr12:83079644-83079654 chr12:83081474-83081492 chr12:83079642-83079655
5	SMARCB1	chr12:83079527-83081684	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr12:83079548-83081869	GM18505	blood:	n/a	n/a
7	RAD21	chr12:83079371-83081744	SK-N-SH_RA	brain:	n/a	chr12:83081480-83081490 chr12:83079640-83079659 chr12:83079645-83079655 chr12:83079522-83079532 chr12:83079645-83079657
8	POLR2A	chr12:83080194-83081193	A549	lung:	n/a	n/a
9	POLR2A	chr12:83079456-83081778	GM12892	blood:	n/a	n/a
10	TAF1	chr12:83079336-83081289	MCF-7	breast:	n/a	n/a
11	POLR2A	chr12:83080760-83081188	A549	lung:	n/a	n/a
12	POLR2A	chr12:83080074-83081240	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr12:83079488-83082182	GM12891	blood:	n/a	n/a
14	RUNX3	chr12:83080787-83081286	GM12878	blood:	n/a	n/a
15	MXI1	chr12:83079361-83081979	IMR90	lung:	n/a	n/a
16	MAX	chr12:83080145-83081715	GM12878	blood:	n/a	chr12:83081461-83081471
17	TCF7L2	chr12:83080899-83081930	Hela-S3	cervix:	n/a	n/a
18	POLR2A	chr12:83080277-83081357	PFSK-1	brain:	n/a	n/a
19	SIN3AK20	chr12:83079411-83081281	MCF-7	breast:	n/a	n/a
20	POLR2A	chr12:83079532-83081898	H1-neurons	neurons:	n/a	n/a
21	POLR2A	chr12:83079413-83082202	GM18951	blood:	n/a	n/a
22	POLR2A	chr12:83079925-83081687	MCF-7	breast:	n/a	n/a
23	RAD21	chr12:83079271-83082452	SK-N-SH	brain:	n/a	chr12:83081480-83081490 chr12:83079640-83079659 chr12:83079645-83079655 chr12:83079522-83079532 chr12:83079645-83079657
24	CTCF	chr12:83079187-83082444	SK-N-SH	brain:	n/a	chr12:83079640-83079656 chr12:83081477-83081490 chr12:83079639-83079657 chr12:83079644-83079654 chr12:83081474-83081492 chr12:83079642-83079655
25	TCF12	chr12:83080779-83081724	ECC-1	luminal epithelium:	n/a	chr12:83080924-83080934 chr12:83081317-83081327
26	MAX	chr12:83080793-83081913	ECC-1	luminal epithelium:	n/a	chr12:83081461-83081471
27	ZNF143	chr12:83079468-83082315	GM12878	blood:	n/a	chr12:83081117-83081127 chr12:83080420-83080435 chr12:83080413-83080431 chr12:83082094-83082103 chr12:83079648-83079658
28	CTCF	chr12:83081040-83081190	GM12867	blood:	n/a	n/a
29	POLR2A	chr12:83080184-83081226	A549	lung:	n/a	n/a
30	MAX	chr12:83080063-83081571	A549	lung:	n/a	chr12:83081461-83081471
31	MAZ	chr12:83079446-83081768	GM12878	blood:	n/a	chr12:83081461-83081471
32	RCOR1	chr12:83080127-83081579	Hela-S3	cervix:	n/a	n/a
33	SIN3A	chr12:83079513-83082116	GM12878	blood:	n/a	chr12:83080351-83080360 chr12:83081477-83081488
34	POLR2A	chr12:83080011-83081190	GM12878	blood:	n/a	n/a
35	POLR2A	chr12:83079565-83081808	GM18526	blood:	n/a	n/a
36	POLR2A	chr12:83080100-83081209	HCT-116	colon:	n/a	n/a
37	MAX	chr12:83080805-83081767	H1-hESC	embryonic stem cell:	n/a	chr12:83081461-83081471
38	MAX	chr12:83080243-83081288	SK-N-SH	brain:	n/a	n/a
39	MAX	chr12:83079508-83081774	Hela-S3	cervix:	n/a	chr12:83081461-83081471
40	MAX	chr12:83079398-83081764	MCF-7	breast:	n/a	chr12:83081461-83081471
41	SIN3AK20	chr12:83080789-83081206	A549	lung:	n/a	n/a
42	POLR2A	chr12:83080368-83081194	A549	lung:	n/a	n/a
43	SIN3AK20	chr12:83079425-83082103	MCF-7	breast:	n/a	n/a
44	POLR2A	chr12:83079406-83081828	GM19193	blood:	n/a	n/a
45	POLR2A	chr12:83080050-83081697	H1-neurons	neurons:	n/a	n/a
46	HA-E2F1	chr12:83079599-83081942	MCF-7	breast:	n/a	chr12:83081051-83081062 chr12:83081052-83081062 chr12:83081054-83081061 chr12:83081054-83081061 chr12:83080662-83080671 chr12:83081053-83081061 chr12:83081054-83081061 chr12:83081053-83081061
47	SIN3A	chr12:83079492-83082264	H1-hESC	embryonic stem cell:	n/a	chr12:83080351-83080360 chr12:83081477-83081488
48	MXI1	chr12:83079214-83083414	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr12:83080152-83081205	A549	lung:	n/a	n/a
50	ELF1	chr12:83080067-83081746	GM12878	blood:	n/a	chr12:83081073-83081082

No.	Distal block	Cell Line	Cell type
1	chr12:83079676..83081707-chr12:83150851..83153057,2	MCF-7	breast:
2	chr12:83079877..83081535-chr12:120728404..120731286,2	MCF-7	breast:
3	chr12:83078982..83081661-chr3:63848631..63850534,2	MCF-7	breast:

Variant related genes	Relation type
TMTC2	TF binding region
ENSG00000163635	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000179104	Chromatin interaction
ENSG00000163634	Chromatin interaction
ENSG00000202538	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10862497	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11115342	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11115348	0.82[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11115353	0.86[EUR][1000 genomes]
rs11115355	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11609532	0.90[EUR][1000 genomes]
rs11614435	0.86[EUR][1000 genomes]
rs12305736	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12307168	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12423043	0.82[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12426166	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13377925	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17009812	0.83[EUR][1000 genomes]
rs17009851	0.82[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17009854	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs17009856	0.82[CEU][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17009882	0.80[EUR][1000 genomes]
rs17009885	0.80[EUR][1000 genomes]
rs1922576	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1922579	0.89[EUR][1000 genomes]
rs4620789	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4882428	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55657485	0.90[EUR][1000 genomes]
rs56298822	0.93[EUR][1000 genomes]
rs56396658	0.90[EUR][1000 genomes]
rs61485473	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6539683	0.86[ASN][1000 genomes]
rs7134747	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7134766	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7135486	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72615654	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7294890	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7303469	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7313778	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73354481	0.83[EUR][1000 genomes]
rs74106267	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961953	0.82[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7975647	0.82[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053093	chr12:82645292-83287809	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv541551	chr12:82645292-83287809	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv559541	chr12:82715210-83108395	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv899348	chr12:82744187-83169297	Enhancers Strong transcription Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv427917	chr12:82917031-83279712	Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv899349	chr12:82931646-83114286	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	esv3348300	chr12:83079532-83086951	Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
9	esv1008305	chr12:83080776-83081231	Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83079400-83081400	Active TSS	Primary T cells from cord blood	blood
2	chr12:83079400-83081800	Active TSS	Hela-S3	cervix
3	chr12:83079400-83082200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:83079400-83082400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:83079400-83084200	Active TSS	Fetal Intestine Large	intestine
6	chr12:83079600-83081400	Active TSS	Duodenum Mucosa	Duodenum
7	chr12:83079600-83081400	Active TSS	Osteobl	bone
8	chr12:83079600-83081600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr12:83079600-83081600	Active TSS	Fetal Intestine Small	intestine
10	chr12:83079600-83081800	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr12:83079600-83081800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:83079600-83081800	Active TSS	Primary T helper naive cells from peripheral blood	blood
13	chr12:83079600-83081800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
14	chr12:83079600-83081800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:83079600-83081800	Active TSS	Fetal Brain Female	brain
16	chr12:83079600-83082000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
17	chr12:83079600-83082000	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr12:83079600-83082000	Active TSS	Primary T killer memory cells from peripheral blood	blood
19	chr12:83079600-83082000	Active TSS	A549	lung
20	chr12:83079600-83082200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:83079600-83082200	Active TSS	H9 Cell Line	embryonic stem cell
22	chr12:83079600-83082200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr12:83079600-83082200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:83079600-83082200	Active TSS	Muscle Satellite Cultured Cells	--
25	chr12:83079600-83082200	Active TSS	Esophagus	oesophagus
26	chr12:83079600-83082200	Active TSS	Pancreas	Pancrea
27	chr12:83079600-83082200	Active TSS	Stomach Mucosa	stomach
28	chr12:83079600-83082200	Active TSS	HSMM	muscle
29	chr12:83079600-83082400	Active TSS	H1 Cell Line	embryonic stem cell
30	chr12:83079600-83082400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:83079600-83082400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr12:83079600-83082400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:83079600-83082400	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr12:83079600-83082400	Active TSS	Right Ventricle	heart
35	chr12:83079600-83082600	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr12:83079600-83082600	Active TSS	Left Ventricle	heart
37	chr12:83079600-83082800	Active TSS	Colonic Mucosa	Colon
38	chr12:83079600-83082800	Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr12:83079600-83082800	Active TSS	Right Atrium	heart
40	chr12:83079600-83082800	Active TSS	NHDF-Ad	bronchial
41	chr12:83079600-83083200	Active TSS	Psoas Muscle	Psoas
42	chr12:83079600-83083600	Active TSS	Stomach Smooth Muscle	stomach
43	chr12:83079600-83083800	Active TSS	Brain Substantia Nigra	brain
44	chr12:83079600-83083800	Active TSS	Duodenum Smooth Muscle	Duodenum
45	chr12:83079600-83083800	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr12:83079600-83084000	Active TSS	Brain Angular Gyrus	brain
47	chr12:83079600-83084000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:83079600-83084000	Active TSS	Colon Smooth Muscle	Colon
49	chr12:83079600-83084200	Active TSS	Brain Anterior Caudate	brain
50	chr12:83079600-83084200	Active TSS	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links