Variant report

Variant	rs3217795
Chromosome Location	chr12:4386064-4386065
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	POLR2A	chr12:4378383-4393977	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:4385965-4389349	MCF10A-Er-Src	breast:	n/a	n/a
3	ZEB1	chr12:4385989-4386461	GM12878	blood:	n/a	n/a
4	SMC3	chr12:4385862-4386526	GM12878	blood:	n/a	chr12:4386279-4386293
5	POLR2A	chr12:4385944-4386661	K562	blood:	n/a	n/a
6	FOXA2	chr12:4386017-4386492	A549	lung:	n/a	n/a
7	POLR2A	chr12:4382575-4386671	PFSK-1	brain:	n/a	n/a
8	TEAD4	chr12:4385923-4386625	SK-N-SH	brain:	n/a	n/a
9	RAD21	chr12:4385940-4386505	Hela-S3	cervix:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
10	FOXM1	chr12:4385850-4386559	GM12878	blood:	n/a	n/a
11	YY1	chr12:4386034-4386434	GM12878	blood:	n/a	n/a
12	CHD2	chr12:4385973-4386429	HepG2	liver:	n/a	n/a
13	ZNF143	chr12:4385980-4386469	K562	blood:	n/a	n/a
14	TEAD4	chr12:4386052-4386505	K562	blood:	n/a	n/a
15	CHD1	chr12:4386026-4386439	H1-hESC	embryonic stem cell:	n/a	n/a
16	EP300	chr12:4386050-4386441	H1-hESC	embryonic stem cell:	n/a	n/a
17	RAD21	chr12:4386050-4386597	A549	lung:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
18	CTCF	chr12:4385988-4386611	MCF-7	breast:	n/a	chr12:4386277-4386295 chr12:4386278-4386294 chr12:4386272-4386293 chr12:4386282-4386290
19	RAD21	chr12:4386062-4386455	A549	lung:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
20	STAT1	chr12:4385975-4386559	GM12878	blood:	n/a	n/a
21	POLR2A	chr12:4385697-4406476	GM12892	blood:	n/a	n/a
22	STAT5A	chr12:4385848-4386487	GM12878	blood:	n/a	n/a
23	SMC3	chr12:4385702-4386630	SK-N-SH	brain:	n/a	chr12:4386279-4386293
24	MXI1	chr12:4385784-4386526	GM12878	blood:	n/a	n/a
25	EP300	chr12:4385893-4386446	K562	blood:	n/a	n/a
26	EP300	chr12:4386059-4386488	HepG2	liver:	n/a	n/a
27	TEAD4	chr12:4385978-4386537	HCT-116	colon:	n/a	n/a
28	YY1	chr12:4386004-4386449	GM12878	blood:	n/a	n/a
29	RAD21	chr12:4385947-4386596	A549	lung:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
30	RAD21	chr12:4385980-4386531	HCT-116	colon:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
31	SIN3A	chr12:4385935-4386532	H1-hESC	embryonic stem cell:	n/a	n/a
32	RELA	chr12:4385962-4386504	GM19099	blood:	n/a	n/a
33	RUNX3	chr12:4385869-4386526	GM12878	blood:	n/a	n/a
34	CHD2	chr12:4385991-4386514	H1-hESC	embryonic stem cell:	n/a	n/a
35	ZNF384	chr12:4386026-4386447	GM12878	blood:	n/a	n/a
36	HNF4G	chr12:4385956-4386487	HepG2	liver:	n/a	chr12:4386208-4386216 chr12:4386350-4386368 chr12:4386352-4386366 chr12:4386352-4386366 chr12:4386353-4386366 chr12:4386353-4386365
37	RAD21	chr12:4385825-4386752	SK-N-SH	brain:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
38	TEAD4	chr12:4386043-4386524	H1-hESC	embryonic stem cell:	n/a	n/a
39	BCLAF1	chr12:4385886-4386513	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:4385653-4386611	SK-N-MC	brain:	n/a	n/a
41	RAD21	chr12:4385999-4386515	MCF-7	breast:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
42	POLR2A	chr12:4385915-4388217	K562	blood:	n/a	n/a
43	CTCF	chr12:4386038-4386522	GM12878	blood:	n/a	chr12:4386277-4386295 chr12:4386278-4386294 chr12:4386272-4386293 chr12:4386282-4386290
44	CHD2	chr12:4385897-4386565	K562	blood:	n/a	n/a
45	RAD21	chr12:4385952-4386520	H1-hESC	embryonic stem cell:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
46	POLR2A	chr12:4377522-4393821	GM19099	blood:	n/a	n/a
47	RELA	chr12:4385902-4386833	GM18951	blood:	n/a	n/a
48	ELF1	chr12:4386046-4386561	GM12878	blood:	n/a	n/a
49	RAD21	chr12:4385913-4386564	IMR90	lung:	n/a	chr12:4386278-4386291 chr12:4386285-4386292 chr12:4386275-4386294
50	CTCF	chr12:4385329-4387466	A549	lung:	n/a	chr12:4386277-4386295 chr12:4386278-4386294 chr12:4386272-4386293 chr12:4386282-4386290

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:
8	chr12:4104787..4105607-chr12:4385997..4386676,2	MCF-7	breast:

Variant related genes	Relation type
CCND2-AS1	TF binding region
CCND2	TF binding region
CCND2-AS2	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]
rs3217792	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3217893	1.00[MEX][hapmap]

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:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4377600-4386200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:4382000-4388000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr12:4383000-4386200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
4	chr12:4383400-4386200	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
5	chr12:4383600-4386400	Active TSS	Brain Angular Gyrus	brain
6	chr12:4384400-4388000	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
7	chr12:4384400-4390600	Weak transcription	Gastric	stomach
8	chr12:4384600-4387000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
9	chr12:4384800-4386600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:4384800-4386600	Transcr. at gene 5' and 3'	Fetal Muscle Leg	muscle
11	chr12:4384800-4388200	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr12:4385000-4386200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:4385000-4386600	Transcr. at gene 5' and 3'	NHEK	skin
14	chr12:4385000-4387000	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr12:4385000-4390000	Transcr. at gene 5' and 3'	Cortex derived primary cultured neurospheres	brain
16	chr12:4385200-4386200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
17	chr12:4385200-4386200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:4385200-4386200	Transcr. at gene 5' and 3'	Primary T helper cells fromperipheralblood	blood
19	chr12:4385200-4386200	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
20	chr12:4385200-4386200	Bivalent Enhancer	Fetal Thymus	thymus
21	chr12:4385200-4386200	Enhancers	Spleen	Spleen
22	chr12:4385200-4386400	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
23	chr12:4385200-4386400	Transcr. at gene 5' and 3'	Rectal Smooth Muscle	rectum
24	chr12:4385200-4386600	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr12:4385200-4386600	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:4385200-4386600	Transcr. at gene 5' and 3'	Fetal Muscle Trunk	muscle
27	chr12:4385200-4386600	Transcr. at gene 5' and 3'	HMEC	breast
28	chr12:4385200-4386800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
29	chr12:4385200-4386800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
30	chr12:4385200-4387000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
31	chr12:4385200-4388200	Transcr. at gene 5' and 3'	Fetal Intestine Large	intestine
32	chr12:4385200-4388400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:4385200-4390800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:4385200-4390800	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
35	chr12:4385200-4391000	Genic enhancers	Sigmoid Colon	Sigmoid Colon
36	chr12:4385400-4386200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr12:4385400-4386200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
38	chr12:4385400-4386200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
39	chr12:4385400-4386200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:4385400-4386200	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr12:4385400-4386200	Transcr. at gene 5' and 3'	Duodenum Smooth Muscle	Duodenum
42	chr12:4385400-4386200	Enhancers	Pancreas	Pancrea
43	chr12:4385400-4386200	Transcr. at gene 5' and 3'	K562	blood
44	chr12:4385400-4386400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:4385400-4386400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:4385400-4386600	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
47	chr12:4385400-4386600	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
48	chr12:4385400-4386600	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
49	chr12:4385400-4386600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:4385400-4386600	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon

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