Variant report

Variant	rs3217794
Chromosome Location	chr12:4385881-4385882
allele	C/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	POLR2A	chr12:4378383-4393977	GM12878	blood:	n/a	n/a
2	SMC3	chr12:4385862-4386526	GM12878	blood:	n/a	chr12:4386279-4386293
3	POLR2A	chr12:4382575-4386671	PFSK-1	brain:	n/a	n/a
4	FOXM1	chr12:4385850-4386559	GM12878	blood:	n/a	n/a
5	POLR2A	chr12:4385697-4406476	GM12892	blood:	n/a	n/a
6	STAT5A	chr12:4385848-4386487	GM12878	blood:	n/a	n/a
7	SMC3	chr12:4385702-4386630	SK-N-SH	brain:	n/a	chr12:4386279-4386293
8	MXI1	chr12:4385784-4386526	GM12878	blood:	n/a	n/a
9	RUNX3	chr12:4385869-4386526	GM12878	blood:	n/a	n/a
10	RAD21	chr12:4385825-4386752	SK-N-SH	brain:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
11	POLR2A	chr12:4385653-4386611	SK-N-MC	brain:	n/a	n/a
12	POLR2A	chr12:4377522-4393821	GM19099	blood:	n/a	n/a
13	CTCF	chr12:4385329-4387466	A549	lung:	n/a	chr12:4386277-4386295 chr12:4386278-4386294 chr12:4386272-4386293 chr12:4386282-4386290
14	POLR2A	chr12:4377442-4388337	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:4384783-4393854	GM12878	blood:	n/a	n/a
16	POLR2A	chr12:4385876-4386651	GM12891	blood:	n/a	n/a
17	POLR2A	chr12:4385857-4388310	GM12892	blood:	n/a	n/a
18	USF2	chr12:4385826-4386751	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:4377597-4393888	GM12891	blood:	n/a	n/a
20	POLR2A	chr12:4385838-4386619	GM12891	blood:	n/a	n/a
21	POLR2A	chr12:4385705-4388341	GM12892	blood:	n/a	n/a
22	ZNF143	chr12:4385848-4386486	GM12878	blood:	n/a	n/a
23	RAD21	chr12:4385843-4386544	GM12878	blood:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
24	POLR2A	chr12:4382739-4388391	H1-hESC	embryonic stem cell:	n/a	n/a
25	MTA3	chr12:4385808-4386653	GM12878	blood:	n/a	n/a
26	WRNIP1	chr12:4384422-4387650	GM12878	blood:	n/a	n/a
27	TBL1XR1	chr12:4385848-4386517	GM12878	blood:	n/a	n/a
28	POLR2A	chr12:4377863-4386616	GM18526	blood:	n/a	n/a
29	POLR2A	chr12:4385820-4386520	H1-hESC	embryonic stem cell:	n/a	n/a
30	MAZ	chr12:4385825-4386481	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:4385780-4388389	GM12892	blood:	n/a	n/a
32	POLR2A	chr12:4385142-4388424	PFSK-1	brain:	n/a	n/a
33	POLR2A	chr12:4377513-4404672	GM12878	blood:	n/a	n/a
34	TBL1XR1	chr12:4385658-4386568	K562	blood:	n/a	n/a
35	POLR2A	chr12:4385126-4393865	K562	blood:	n/a	n/a
36	CTCF	chr12:4385820-4385970	SK-N-SH_RA	brain:	n/a	n/a
37	MAX	chr12:4385634-4386443	GM12878	blood:	n/a	n/a
38	POLR2A	chr12:4377772-4388270	GM19193	blood:	n/a	n/a
39	ZNF263	chr12:4385784-4386560	HEK293-T-REx	kidney:	n/a	chr12:4386165-4386174
40	POLR2A	chr12:4385814-4387591	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:3994703..3995335-chr12:4385793..4386765,3	MCF-7	breast:
2	chr12:4216455..4217156-chr12:4385829..4386409,2	MCF-7	breast:
3	chr12:4216482..4217070-chr12:4385866..4386804,2	NB4	blood:
4	chr12:4104755..4105582-chr12:4385820..4386626,2	K562	blood:
5	chr12:4216655..4217210-chr12:4385805..4386330,2	K562	blood:
6	chr11:818755..819637-chr12:4385344..4386078,2	NB4	blood:
7	chr12:3992395..3993001-chr12:4385802..4386611,2	MCF-7	breast:

Variant related genes	Relation type
CCND2-AS1	TF binding region
CCND2-AS2	TF binding region
CCND2	TF binding region
ENSG00000177666	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2909382	1.00[AMR][1000 genomes]
rs7972349	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530520	chr12:3726841-4601757	Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1050474	chr12:4226760-4389238	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv832317	chr12:4315298-4435615	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv541360	chr12:4338851-4389238	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv541361	chr12:4362258-4413849	Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
6	esv275173	chr12:4385592-4386221	Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4377600-4386000	Active TSS	Aorta	Aorta
2	chr12:4377600-4386200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:4382000-4388000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
4	chr12:4382200-4386000	Active TSS	Right Atrium	heart
5	chr12:4383000-4386200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
6	chr12:4383400-4386000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
7	chr12:4383400-4386200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
8	chr12:4383600-4386400	Active TSS	Brain Angular Gyrus	brain
9	chr12:4384400-4388000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
10	chr12:4384400-4390600	Weak transcription	Gastric	stomach
11	chr12:4384600-4387000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
12	chr12:4384800-4386600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:4384800-4386600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
14	chr12:4384800-4388200	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr12:4385000-4386200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:4385000-4386600	Transcr. at gene 5' and 3'	NHEK	skin
17	chr12:4385000-4387000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:4385000-4390000	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
19	chr12:4385200-4386000	Transcr. at gene 5' and 3'	Primary T cells fromperipheralblood	blood
20	chr12:4385200-4386000	Transcr. at gene 5' and 3'	Fetal Brain Male	brain
21	chr12:4385200-4386000	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
22	chr12:4385200-4386000	Weak transcription	Small Intestine	intestine
23	chr12:4385200-4386200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
24	chr12:4385200-4386200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:4385200-4386200	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
26	chr12:4385200-4386200	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
27	chr12:4385200-4386200	Bivalent Enhancer	Fetal Thymus	thymus
28	chr12:4385200-4386200	Enhancers	Spleen	Spleen
29	chr12:4385200-4386400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
30	chr12:4385200-4386400	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
31	chr12:4385200-4386600	Genic enhancers	Primary B cells from peripheral blood	blood
32	chr12:4385200-4386600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:4385200-4386600	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
34	chr12:4385200-4386600	Transcr. at gene 5' and 3'	HMEC	breast
35	chr12:4385200-4386800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
36	chr12:4385200-4386800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
37	chr12:4385200-4387000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
38	chr12:4385200-4388200	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
39	chr12:4385200-4388400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr12:4385200-4390800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr12:4385200-4390800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
42	chr12:4385200-4391000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
43	chr12:4385400-4386000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr12:4385400-4386000	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:4385400-4386000	Transcr. at gene 5' and 3'	Primary T helper memory cells from peripheral blood 1	blood
46	chr12:4385400-4386000	Flanking Active TSS	Fetal Heart	heart
47	chr12:4385400-4386000	Weak transcription	Right Ventricle	heart
48	chr12:4385400-4386000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
49	chr12:4385400-4386200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr12:4385400-4386200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell

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