Variant report

Variant	rs12315734
Chromosome Location	chr12:49414023-49414024
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:150)
CpG islands
(count:0)
Chromatin interactive
region (count:25)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:150 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:49413880-49414030	GM12801	blood:	n/a	n/a
2	RAD21	chr12:49413932-49414041	HepG2	liver:	n/a	n/a
3	CTCF	chr12:49413880-49414030	HPAF	blood vessel:	n/a	n/a
4	CTCF	chr12:49413940-49414090	GM12869	blood:	n/a	n/a
5	CTCF	chr12:49413900-49414050	A549	lung:	n/a	n/a
6	CTCF	chr12:49413858-49414049	A549	lung:	n/a	n/a
7	CTCF	chr12:49413880-49414030	Hela-S3	cervix:	n/a	n/a
8	CTCF	chr12:49413864-49414043	GM13977	blood:	n/a	n/a
9	CTCF	chr12:49413793-49414082	K562	blood:	n/a	n/a
10	CTCF	chr12:49413880-49414030	GM12873	blood:	n/a	n/a
11	POLR2A	chr12:49411497-49414182	K562	blood:	n/a	n/a
12	CTCF	chr12:49413662-49414119	K562	blood:	n/a	n/a
13	CTCF	chr12:49413900-49414050	GM12874	blood:	n/a	n/a
14	CTCF	chr12:49413880-49414030	BJ	skin:	n/a	n/a
15	HDAC2	chr12:49413765-49414050	K562	blood:	n/a	n/a
16	CTCF	chr12:49413880-49414030	AG10803	skin:	n/a	n/a
17	CTCF	chr12:49413856-49414066	Medullo	brain:	n/a	n/a
18	POLR2A	chr12:49411493-49414082	H1-hESC	embryonic stem cell:	n/a	n/a
19	CTCF	chr12:49413767-49414078	K562	blood:	n/a	n/a
20	CTCF	chr12:49413811-49414113	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr12:49413825-49414051	A549	lung:	n/a	n/a
22	CTCF	chr12:49413873-49414023	ProgFib	skin:	n/a	n/a
23	CTCF	chr12:49413840-49414062	GM12891	blood:	n/a	n/a
24	CTCF	chr12:49413880-49414030	GM12874	blood:	n/a	n/a
25	CTCF	chr12:49413757-49414137	K562	blood:	n/a	n/a
26	RAD21	chr12:49413812-49414060	A549	lung:	n/a	n/a
27	CTCF	chr12:49413878-49414026	GM20000	blood:	n/a	n/a
28	MAX	chr12:49413861-49414028	K562	blood:	n/a	n/a
29	CTCF	chr12:49413880-49414030	GM06990	blood:	n/a	n/a
30	CTCF	chr12:49413888-49414038	GM13976	blood:	n/a	n/a
31	CTCF	chr12:49413880-49414030	HPF	lung:	n/a	n/a
32	CTCF	chr12:49413900-49414050	RPTEC	kidney:	n/a	n/a
33	CTCF	chr12:49413823-49414080	K562	blood:	n/a	n/a
34	CTCF	chr12:49413920-49414070	HRPEpiC	eye:	n/a	n/a
35	CTCF	chr12:49413900-49414050	HCPEpiC	choroid plexus:	n/a	n/a
36	CTCF	chr12:49413900-49414050	SK-N-SH_RA	brain:	n/a	n/a
37	CTCF	chr12:49413880-49414030	HEEpiC	esophagus:	n/a	n/a
38	POLR2A	chr12:49411424-49414153	PFSK-1	brain:	n/a	n/a
39	YY1	chr12:49413776-49414049	GM12878	blood:	n/a	n/a
40	CTCF	chr12:49413880-49414030	WERI-Rb-1	eye:	n/a	n/a
41	CTCF	chr12:49413837-49414068	Hela-S3	cervix:	n/a	n/a
42	MAZ	chr12:49413760-49414114	K562	blood:	n/a	n/a
43	MXI1	chr12:49410957-49414233	SK-N-SH	brain:	n/a	n/a
44	CTCF	chr12:49413880-49414030	GM12875	blood:	n/a	n/a
45	CTCF	chr12:49413880-49414030	K562	blood:	n/a	n/a
46	CTCF	chr12:49413900-49414050	AG04450	lung:	n/a	n/a
47	CBX3	chr12:49413722-49414092	K562	blood:	n/a	n/a
48	CTCF	chr12:49413900-49414050	GM06990	blood:	n/a	n/a
49	SPI1	chr12:49413737-49414064	HL-60	blood:	n/a	n/a
50	ELF1	chr12:49413734-49414046	K562	blood:	n/a	n/a

No data

(count:25 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49411250..49414905-chr12:49447359..49450802,6	MCF-7	breast:
2	chr12:49408415..49414757-chr12:49522619..49525582,9	MCF-7	breast:
3	chr12:49410741..49414968-chr12:49656213..49660641,6	K562	blood:
4	chr12:49408338..49419708-chr12:49447252..49460551,38	K562	blood:
5	chr12:49348804..49352502-chr12:49411258..49414497,4	MCF-7	breast:
6	chr12:49412238..49414069-chr12:49657738..49659294,2	MCF-7	breast:
7	chr12:49349202..49351999-chr12:49410599..49414055,4	MCF-7	breast:
8	chr12:49361132..49362678-chr12:49413782..49415312,2	MCF-7	breast:
9	chr12:49412434..49414037-chr12:49481965..49485048,3	K562	blood:
10	chr12:49368203..49373775-chr12:49410781..49415457,6	K562	blood:
11	chr12:49207853..49210267-chr12:49412242..49414195,2	K562	blood:
12	chr12:49410733..49415536-chr12:49523564..49526910,8	K562	blood:
13	chr12:49412487..49414498-chr12:49429302..49431280,2	MCF-7	breast:
14	chr12:49369680..49374710-chr12:49411684..49416052,5	K562	blood:
15	chr12:49411035..49414032-chr12:49431081..49434275,3	K562	blood:
16	chr12:49109260..49113049-chr12:49411417..49414170,4	K562	blood:
17	chr12:49409658..49414587-chr12:49499656..49504173,4	K562	blood:
18	chr12:49409714..49416851-chr12:49447402..49455499,24	MCF-7	breast:
19	chr12:49390223..49391069-chr12:49413217..49414800,4	K562	blood:
20	chr12:49407466..49416688-chr12:49451532..49456163,12	MCF-7	breast:
21	chr12:49411020..49415552-chr12:49523211..49527183,13	K562	blood:
22	chr12:49410141..49415550-chr12:49657481..49661686,9	K562	blood:
23	chr12:49209305..49214344-chr12:49410836..49414443,6	MCF-7	breast:
24	chr12:49410463..49414527-chr12:49462417..49465664,5	K562	blood:
25	chr12:49412128..49415221-chr12:49522907..49525212,5	MCF-7	breast:

No data

Variant related genes	Relation type
PRKAG1	TF binding region
ENSG00000200303	Chromatin interaction
ENSG00000129315	Chromatin interaction
ENSG00000125084	Chromatin interaction
ENSG00000139636	Chromatin interaction
ENSG00000167550	Chromatin interaction
ENSG00000167535	Chromatin interaction
ENSG00000272822	Chromatin interaction
ENSG00000123416	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000258101	Chromatin interaction
ENSG00000200309	Chromatin interaction
ENSG00000167548	Chromatin interaction
ENSG00000258017	Chromatin interaction
ENSG00000257346	Chromatin interaction
ENSG00000134287	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11168820	1.00[AMR][1000 genomes]
rs11168821	1.00[AMR][1000 genomes]
rs11168823	1.00[AMR][1000 genomes]
rs11168824	1.00[AMR][1000 genomes]
rs11168826	1.00[AMR][1000 genomes]
rs12303646	1.00[AMR][1000 genomes]
rs12304391	0.82[ASW][hapmap];1.00[AMR][1000 genomes]
rs12309341	0.82[ASW][hapmap];1.00[AMR][1000 genomes]
rs12318316	1.00[MEX][hapmap]
rs13377622	0.82[ASW][hapmap]
rs13377924	1.00[AMR][1000 genomes]
rs13377927	1.00[AMR][1000 genomes]
rs4018512	0.82[ASW][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
4	nsv558833	chr12:49358880-49478812	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
6	esv3387384	chr12:49412035-49416433	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	38 gene(s)	inside rSNPs	diseases
7	esv3397588	chr12:49413110-49415658	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases
8	esv3354957	chr12:49413735-49414983	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49412600-49415000	Weak transcription	Gastric	stomach
2	chr12:49413000-49414600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:49413000-49414600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr12:49413000-49414600	Weak transcription	Lung	lung
5	chr12:49413000-49414600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr12:49413000-49415000	Weak transcription	Esophagus	oesophagus
7	chr12:49413000-49415000	Weak transcription	Pancreas	Pancrea
8	chr12:49413000-49415200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr12:49413000-49415200	Weak transcription	Aorta	Aorta
10	chr12:49413000-49415200	Weak transcription	Brain Substantia Nigra	brain
11	chr12:49413000-49415200	Weak transcription	Rectal Smooth Muscle	rectum
12	chr12:49413000-49415600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:49413000-49416000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr12:49413000-49453400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr12:49413200-49414200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:49413200-49414200	Enhancers	Primary B cells from cord blood	blood
17	chr12:49413200-49414200	Enhancers	Fetal Muscle Leg	muscle
18	chr12:49413200-49414400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr12:49413200-49414400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:49413200-49414400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr12:49413200-49414400	Weak transcription	NHLF	lung
22	chr12:49413200-49414600	Weak transcription	Ovary	ovary
23	chr12:49413200-49415000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr12:49413200-49415200	Weak transcription	Right Ventricle	heart
25	chr12:49413200-49415200	Weak transcription	Small Intestine	intestine
26	chr12:49413200-49415800	Weak transcription	HMEC	breast
27	chr12:49413200-49421400	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr12:49413200-49424800	Weak transcription	Right Atrium	heart
29	chr12:49413400-49414200	Weak transcription	Fetal Brain Female	brain
30	chr12:49413400-49414400	Weak transcription	Brain Hippocampus Middle	brain
31	chr12:49413400-49414400	Weak transcription	Colonic Mucosa	Colon
32	chr12:49413400-49414400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr12:49413400-49414600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:49413400-49414600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr12:49413400-49414600	Weak transcription	Brain Anterior Caudate	brain
36	chr12:49413400-49421600	Weak transcription	Stomach Mucosa	stomach
37	chr12:49413400-49449000	Strong transcription	Fetal Intestine Small	intestine
38	chr12:49413600-49414400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:49413600-49414400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr12:49413600-49414400	Weak transcription	Fetal Stomach	stomach
41	chr12:49413600-49414400	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr12:49413600-49414600	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr12:49413600-49414600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr12:49413600-49414600	Weak transcription	Primary T cells from cord blood	blood
45	chr12:49413600-49414600	Weak transcription	Adipose Nuclei	Adipose
46	chr12:49413600-49414600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr12:49413600-49414600	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:49413600-49414600	Weak transcription	HSMMtube	muscle
49	chr12:49413600-49414800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr12:49413600-49414800	Enhancers	Primary hematopoietic stem cells	blood

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