Variant report

Variant	rs3021529
Chromosome Location	chr12:63545680-63545681
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	CTCF	chr12:63545640-63545790	GM12871	blood:	n/a	n/a
2	POLR2A	chr12:63545077-63545698	H1-neurons	neurons:	n/a	n/a
3	CTCF	chr12:63545640-63545790	GM12868	blood:	n/a	n/a
4	REST	chr12:63545618-63546027	ECC-1	luminal epithelium:	n/a	chr12:63545777-63545786
5	REST	chr12:63545614-63545961	PANC-1	pancreas:	n/a	chr12:63545777-63545786
6	EBF1	chr12:63545554-63545709	GM12878	blood:	n/a	n/a
7	E2F6	chr12:63543589-63545750	H1-hESC	embryonic stem cell:	n/a	chr12:63544721-63544732 chr12:63545655-63545662 chr12:63543862-63543877 chr12:63544722-63544733 chr12:63544721-63544731 chr12:63545113-63545120 chr12:63545655-63545662 chr12:63544722-63544729 chr12:63545113-63545120 chr12:63544722-63544730 chr12:63544722-63544730 chr12:63543759-63543774 chr12:63545113-63545120 chr12:63545655-63545662
8	CTCF	chr12:63545677-63545772	A549	lung:	n/a	n/a
9	CTCF	chr12:63545560-63545710	WI-38	lung:	n/a	n/a
10	CTCF	chr12:63545621-63546650	A549	lung:	n/a	chr12:63546025-63546038
11	SIN3A	chr12:63543863-63546155	H1-hESC	embryonic stem cell:	n/a	n/a
12	CTCF	chr12:63545580-63545730	AG04450	lung:	n/a	n/a
13	CTCF	chr12:63545648-63545813	Fibrobl	skin:	n/a	n/a
14	REST	chr12:63545582-63545970	ECC-1	luminal epithelium:	n/a	chr12:63545777-63545786
15	CTCF	chr12:63545667-63545757	Gliobla	brain:	n/a	n/a
16	REST	chr12:63545447-63546201	A549	lung:	n/a	chr12:63545777-63545786
17	CTCF	chr12:63545600-63545750	WI-38	lung:	n/a	n/a
18	CTCF	chr12:63545648-63546263	MCF-7	breast:	n/a	chr12:63546025-63546038
19	CTCF	chr12:63545620-63545770	GM12878	blood:	n/a	n/a
20	REST	chr12:63545673-63545999	SK-N-SH	brain:	n/a	chr12:63545777-63545786
21	POLR2A	chr12:63545003-63545754	H1-neurons	neurons:	n/a	n/a
22	CTCF	chr12:63545680-63545830	GM12874	blood:	n/a	n/a
23	REST	chr12:63544707-63546100	H1-neurons	neurons:	n/a	chr12:63545053-63545066 chr12:63545777-63545786
24	ZNF263	chr12:63544346-63546142	HEK293-T-REx	kidney:	n/a	chr12:63545887-63545896
25	CTCF	chr12:63545680-63545830	GM12866	blood:	n/a	n/a
26	CTCF	chr12:63545680-63545830	HUVEC	blood vessel:	n/a	n/a
27	KAP1	chr12:63544476-63546436	HEK293	kidney:	n/a	n/a
28	REST	chr12:63545634-63545904	Hela-S3	cervix:	n/a	chr12:63545777-63545786

No.	Distal block	Cell Line	Cell type
1	chr12:63545428..63546206-chr12:63674883..63675724,2	MCF-7	breast:
2	chr12:63545448..63546470-chr12:63670124..63671316,6	MCF-7	breast:
3	chr12:63545419..63546376-chr12:64195555..64196413,2	MCF-7	breast:
4	chr12:63545559..63546473-chr12:63669896..63671149,5	MCF-7	breast:

Variant related genes	Relation type
AVPR1A	TF binding region

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10877968	0.91[CEU][hapmap];0.86[MEX][hapmap]
rs11174805	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174806	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11174811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1580704	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1580705	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1587097	0.96[ASN][1000 genomes]
rs1587098	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17099021	0.91[ASN][1000 genomes]
rs17099023	0.91[ASN][1000 genomes]
rs34462214	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3803107	0.91[CEU][hapmap]
rs7131747	0.91[ASN][1000 genomes]
rs7308855	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7312429	0.91[ASN][1000 genomes]
rs73138772	0.91[ASN][1000 genomes]
rs73138773	0.91[ASN][1000 genomes]
rs73138776	0.87[ASN][1000 genomes]
rs73140755	0.91[ASN][1000 genomes]
rs73140757	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3415227	chr12:63228121-63591615	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
3	nsv469592	chr12:63486510-63679139	Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv482578	chr12:63486510-63679139	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv832436	chr12:63503993-63658112	Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1035736	chr12:63526274-63920372	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv541510	chr12:63526274-63920372	Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	esv2761742	chr12:63537412-63582333	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1035231	chr12:63537412-63582333	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv899164	chr12:63540476-63611633	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63543200-63546400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr12:63543600-63545800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
3	chr12:63543600-63546000	Flanking Active TSS	Pancreas	Pancrea
4	chr12:63543600-63546000	Bivalent/Poised TSS	Psoas Muscle	Psoas
5	chr12:63543600-63546000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
6	chr12:63543800-63546000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
7	chr12:63543800-63546000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr12:63543800-63546000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
9	chr12:63543800-63546000	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
10	chr12:63543800-63546000	Active TSS	Aorta	Aorta
11	chr12:63543800-63546000	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
12	chr12:63543800-63546000	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
13	chr12:63543800-63546000	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
14	chr12:63543800-63546000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
15	chr12:63543800-63546000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
16	chr12:63543800-63546000	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
17	chr12:63543800-63546200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
18	chr12:63543800-63546200	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
19	chr12:63543800-63546800	Flanking Active TSS	Liver	Liver
20	chr12:63544000-63545800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr12:63544000-63546000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
22	chr12:63544000-63546000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
23	chr12:63544000-63546000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
24	chr12:63544000-63546000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:63544000-63546000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:63544000-63546000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:63544000-63546000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr12:63544200-63545800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
29	chr12:63544200-63545800	Flanking Active TSS	Right Ventricle	heart
30	chr12:63544200-63546000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr12:63544200-63546000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells	blood
32	chr12:63544200-63546000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:63544200-63546000	Bivalent Enhancer	Placenta	Placenta
34	chr12:63544200-63546000	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
35	chr12:63544200-63546000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
36	chr12:63544200-63546000	Flanking Bivalent TSS/Enh	NH-A	brain
37	chr12:63544200-63546200	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
38	chr12:63544200-63546400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
39	chr12:63544200-63546400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
40	chr12:63544400-63545800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
41	chr12:63544400-63546000	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr12:63544400-63546000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
43	chr12:63544400-63546200	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
44	chr12:63544600-63545800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr12:63544600-63545800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
46	chr12:63544600-63546000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
47	chr12:63544600-63546000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
48	chr12:63544600-63546000	Bivalent/Poised TSS	Ovary	ovary
49	chr12:63544600-63546200	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr12:63544800-63545800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain

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