Variant report

Variant	rs12813848
Chromosome Location	chr12:30949637-30949638
allele	C/T
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	chr12:30948756-30949648	H1-hESC	embryonic stem cell:	n/a	chr12:30949347-30949356
2	NRF1	chr12:30949084-30949863	SK-N-SH	brain:	n/a	chr12:30949342-30949351
3	MAX	chr12:30947908-30949830	ECC-1	luminal epithelium:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
4	POLR2A	chr12:30947455-30950217	HUVEC	blood vessel:	n/a	n/a
5	ZBTB7A	chr12:30947681-30950078	ECC-1	luminal epithelium:	n/a	chr12:30948413-30948420
6	E2F4	chr12:30949514-30949701	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr12:30947518-30949699	U87	brain:	n/a	n/a
8	POLR2A	chr12:30947579-30950081	HUVEC	blood vessel:	n/a	n/a
9	MAZ	chr12:30948947-30949675	HepG2	liver:	n/a	chr12:30949347-30949356
10	MYC	chr12:30947622-30949655	Hela-S3	cervix:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
11	MAX	chr12:30947459-30950381	A549	lung:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
12	ZNF263	chr12:30948167-30950323	HEK293-T-REx	kidney:	n/a	chr12:30949957-30949966
13	POLR2A	chr12:30948030-30949713	ECC-1	luminal epithelium:	n/a	n/a
14	MAX	chr12:30947836-30949690	SK-N-SH	brain:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
15	POLR2A	chr12:30947330-30950355	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr12:30948002-30949714	ECC-1	luminal epithelium:	n/a	n/a
17	E2F6	chr12:30948328-30949714	H1-hESC	embryonic stem cell:	n/a	chr12:30949341-30949351 chr12:30949269-30949279 chr12:30949210-30949219 chr12:30948414-30948426
18	TBP	chr12:30947584-30950261	Hela-S3	cervix:	n/a	n/a
19	SRF	chr12:30947970-30949708	ECC-1	luminal epithelium:	n/a	n/a
20	RAD21	chr12:30947815-30949736	ECC-1	luminal epithelium:	n/a	n/a
21	POLR2A	chr12:30947972-30949758	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr12:30947377-30950489	U87	brain:	n/a	n/a
23	PBX3	chr12:30947739-30949691	SK-N-SH	brain:	n/a	n/a
24	MAX	chr12:30947695-30949828	ECC-1	luminal epithelium:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
25	CREB1	chr12:30948038-30949721	A549	lung:	n/a	chr12:30948521-30948534
26	MAX	chr12:30947476-30949646	Hela-S3	cervix:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
27	POLR2A	chr12:30947604-30950324	IMR90	lung:	n/a	n/a
28	JUND	chr12:30947577-30949715	SK-N-SH	brain:	n/a	chr12:30948296-30948307 chr12:30948298-30948307 chr12:30948078-30948088 chr12:30948078-30948088 chr12:30948297-30948306 chr12:30948078-30948088 chr12:30948078-30948088
29	EP300	chr12:30947385-30949871	ECC-1	luminal epithelium:	n/a	chr12:30949342-30949351 chr12:30949708-30949717 chr12:30948297-30948306 chr12:30947657-30947667
30	POLR2A	chr12:30948072-30949651	ProgFib	skin:	n/a	n/a
31	SMARCC1	chr12:30947538-30949652	Hela-S3	cervix:	n/a	chr12:30948297-30948306
32	POLR2A	chr12:30947335-30949674	HUVEC	blood vessel:	n/a	n/a
33	TEAD4	chr12:30947662-30949722	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr12:30948071-30949693	H1-hESC	embryonic stem cell:	n/a	n/a
35	MAX	chr12:30947501-30950261	Hela-S3	cervix:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356
36	CHD2	chr12:30947585-30950215	Hela-S3	cervix:	n/a	chr12:30949618-30949628 chr12:30949531-30949541
37	GATA3	chr12:30947633-30950364	SK-N-SH	brain:	n/a	chr12:30949444-30949451 chr12:30948045-30948052 chr12:30948040-30948056
38	MAX	chr12:30948766-30949650	K562	blood:	n/a	chr12:30949347-30949356
39	SIN3A	chr12:30948199-30949681	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr12:30947452-30950270	Hela-S3	cervix:	n/a	n/a
41	RFX5	chr12:30947620-30949645	Hela-S3	cervix:	n/a	n/a
42	TCF12	chr12:30947662-30949734	ECC-1	luminal epithelium:	n/a	chr12:30948696-30948706
43	POLR2A	chr12:30947443-30949680	HUVEC	blood vessel:	n/a	n/a
44	POLR2A	chr12:30948116-30949645	A549	lung:	n/a	n/a
45	POLR2A	chr12:30947794-30949698	PANC-1	pancreas:	n/a	n/a
46	POLR2A	chr12:30947601-30949661	HCT-116	colon:	n/a	n/a
47	POLR2A	chr12:30947532-30950256	Hela-S3	cervix:	n/a	n/a
48	TCF12	chr12:30947669-30949892	ECC-1	luminal epithelium:	n/a	chr12:30948696-30948706
49	POLR2A	chr12:30947383-30950297	U87	brain:	n/a	n/a
50	MAX	chr12:30947706-30949695	SK-N-SH	brain:	n/a	chr12:30948363-30948372 chr12:30948105-30948115 chr12:30948297-30948306 chr12:30949347-30949356

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:30949617-30949667	HIPEpiC	eye:	n/a
2	chr12:30949617-30949667	GM12878	blood:	n/a
3	chr12:30949617-30949667	NHBE	bronchial:	n/a
4	chr12:30949617-30949667	HEEpiC	esophagus:	n/a
5	chr12:30949617-30949667	RPTEC	kidney:	n/a
6	chr12:30949617-30949667	A549	lung:	n/a
7	chr12:30949617-30949667	MCF10A-Er-Src	breast:	n/a
8	chr12:30949617-30949667	H1-hESC	embryonic stem cell:	embryo
9	chr12:30949617-30949667	BJ	skin:	n/a
10	chr12:30949617-30949667	T-47D	breast:	n/a
11	chr12:30949617-30949667	HCPEpiC	choroid plexus:	n/a
12	chr12:30949617-30949667	ECC-1	luminal epithelium:	n/a
13	chr12:30949617-30949667	K562	blood:	n/a
14	chr12:30949617-30949667	PrEC	prostate:	n/a
15	chr12:30949617-30949667	AG04450	lung:	fetal
16	chr12:30949617-30949667	Jurkat	blood:	n/a
17	chr12:30949617-30949667	HEK293	kidney:	embryo
18	chr12:30949617-30949667	HRE	kidney:	n/a
19	chr12:30949617-30949667	LNCaP	prostate:	n/a
20	chr12:30949617-30949667	NHDF-neo	bronchial:	n/a
21	chr12:30949617-30949667	ovcar-3	ovarian:	n/a
22	chr12:30949617-30949667	HepG2	liver:	n/a
23	chr12:30949617-30949667	IMR90	lung:	fetal
24	chr12:30949617-30949667	AG10803	skin:	n/a
25	chr12:30949617-30949667	GM06990	blood:	n/a
26	chr12:30949617-30949667	GM12891	blood:	n/a
27	chr12:30949617-30949667	HAEpiC	amniotic membrane:	n/a
28	chr12:30949617-30949667	GM12892	blood:	n/a
29	chr12:30949617-30949667	HUVEC	blood vessel:	n/a
30	chr12:30949617-30949667	SKMC	muscle:	n/a
31	chr12:30949617-30949667	AG09319	gingival:	n/a
32	chr12:30949617-30949667	ProgFib	skin:	n/a
33	chr12:30949617-30949667	PFSK-1	brain:	n/a
34	chr12:30949617-30949667	Caco-2	colon:	n/a
35	chr12:30949617-30949667	GM19239	blood:	n/a
36	chr12:30949617-30949667	AG04449	skin:	fetal
37	chr12:30949617-30949667	HCT-116	colon:	n/a
38	chr12:30949617-30949667	PANC-1	pancreas:	n/a
39	chr12:30949617-30949667	HPAEpiC	pulmonary alveolar:	n/a
40	chr12:30949617-30949667	SK-N-SH_RA	brain:	n/a
41	chr12:30949617-30949667	NH-A	brain:	n/a
42	chr12:30949617-30949667	HNPCEpiC	eye:	n/a
43	chr12:30949617-30949667	MCF-7	breast:	n/a
44	chr12:30949617-30949667	U87	brain:	n/a
45	chr12:30949617-30949667	HRCEpiC	kidney:	n/a
46	chr12:30949617-30949667	AG09309	skin:	n/a
47	chr12:30949617-30949667	SK-N-SH	brain:	n/a
48	chr12:30949617-30949667	HMEC	breast:	n/a
49	chr12:30949617-30949667	AoSMC	blood vessel:	n/a
50	chr12:30949617-30949667	Hela-S3	cervix:	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:30906304..30909589-chr12:30948532..30951386,3	K562	blood:
2	chr12:30949150..30949851-chr4:92369989..92370606,2	Hela-S3	cervix:
3	chr12:30949301..30951122-chr12:30954767..30957062,2	MCF-7	breast:
4	chr12:30949445..30950276-chr9:2015332..2016130,2	Hela-S3	cervix:

Variant related genes	Relation type
LINC00941	TF binding region
LINC00941	CpG island
ENSG00000110888	Chromatin interaction
ENSG00000246331	Chromatin interaction
ENSG00000080503	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11051093	0.88[EUR][1000 genomes]
rs12231427	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12816259	0.88[EUR][1000 genomes]
rs12817877	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12818018	0.88[EUR][1000 genomes]
rs12819901	0.88[EUR][1000 genomes]
rs12821717	0.88[EUR][1000 genomes]
rs12821941	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12822194	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12828652	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs12831234	0.88[EUR][1000 genomes]
rs12831356	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs12831687	0.86[EUR][1000 genomes]
rs12832973	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12833211	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16906802	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs34681447	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6487941	0.88[EUR][1000 genomes]
rs6487943	0.88[EUR][1000 genomes]
rs6487944	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7137488	0.88[EUR][1000 genomes]
rs7138448	0.86[EUR][1000 genomes]
rs7296510	0.88[EUR][1000 genomes]
rs7300659	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7301387	1.00[CEU][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs7309444	1.00[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs7312207	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7313984	0.88[EUR][1000 genomes]
rs7314095	0.82[EUR][1000 genomes]
rs7314252	0.86[EUR][1000 genomes]
rs7314420	0.87[EUR][1000 genomes]
rs7314518	0.88[EUR][1000 genomes]
rs7314809	0.88[EUR][1000 genomes]
rs7314917	0.88[EUR][1000 genomes]
rs7314922	0.88[EUR][1000 genomes]
rs7954753	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7954756	0.88[EUR][1000 genomes]
rs7954836	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7969565	0.85[EUR][1000 genomes]
rs7975708	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7975750	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3343291	chr12:30455597-30992837	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv832361	chr12:30794030-30997241	Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv949148	chr12:30800040-31131712	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv34091	chr12:30927650-31061815	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12813848	IPO8	cis	cerebellum	SCAN
rs12813848	LINC00941	cis	Nerve Tibial	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:30947600-30950200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:30947800-30949800	Flanking Active TSS	Primary hematopoietic stem cells	blood
3	chr12:30948000-30950000	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr12:30948000-30950000	Active TSS	Hela-S3	cervix
5	chr12:30948000-30950200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:30948000-30950400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr12:30948200-30949800	Active TSS	Brain Angular Gyrus	brain
8	chr12:30948200-30949800	Active TSS	Right Atrium	heart
9	chr12:30948200-30950000	Active TSS	H9 Cell Line	embryonic stem cell
10	chr12:30948200-30950000	Bivalent Enhancer	Fetal Brain Male	brain
11	chr12:30948200-30950000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
12	chr12:30948200-30950400	Active TSS	iPS-15b Cell Line	embryonic stem cell
13	chr12:30948200-30950400	Active TSS	Brain Anterior Caudate	brain
14	chr12:30948400-30949800	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
15	chr12:30948400-30949800	Active TSS	Brain Substantia Nigra	brain
16	chr12:30948400-30949800	Bivalent/Poised TSS	Fetal Lung	lung
17	chr12:30948400-30949800	Active TSS	Left Ventricle	heart
18	chr12:30948400-30949800	Active TSS	Right Ventricle	heart
19	chr12:30948400-30950000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:30948400-30950000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
21	chr12:30948400-30950000	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
22	chr12:30948400-30950000	Flanking Bivalent TSS/Enh	Placenta	Placenta
23	chr12:30948400-30950200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr12:30948400-30950200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr12:30948400-30950200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:30948400-30950200	Active TSS	Aorta	Aorta
27	chr12:30948400-30950200	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
28	chr12:30948400-30950200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
29	chr12:30948400-30950200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
30	chr12:30948400-30950200	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
31	chr12:30948400-30950200	Active TSS	HSMMtube	muscle
32	chr12:30948400-30950400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
33	chr12:30948400-30950400	Active TSS	Pancreatic Islets	Pancreatic Islet
34	chr12:30948600-30949800	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr12:30948600-30949800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:30948600-30949800	Bivalent/Poised TSS	Fetal Brain Female	brain
37	chr12:30948600-30949800	Bivalent/Poised TSS	Fetal Intestine Small	intestine
38	chr12:30948600-30949800	Active TSS	Fetal Kidney	kidney
39	chr12:30948600-30949800	Active TSS	NHDF-Ad	bronchial
40	chr12:30948600-30950000	Bivalent Enhancer	Primary B cells from cord blood	blood
41	chr12:30948600-30950200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
42	chr12:30948600-30950200	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
43	chr12:30948600-30950400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr12:30948600-30950400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:30948600-30950400	Active TSS	A549	lung
46	chr12:30948600-30950400	Active TSS	Osteobl	bone
47	chr12:30948800-30949800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:30948800-30949800	Active TSS	Ovary	ovary
49	chr12:30948800-30950000	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr12:30948800-30950000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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