Variant report

Variant	rs12036717
Chromosome Location	chr1:224034203-224034204
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	CHD2	chr1:224032925-224034617	Hela-S3	cervix:	n/a	chr1:224033803-224033813
2	POLR2A	chr1:224033433-224034227	Raji	blood:	n/a	n/a
3	TBL1XR1	chr1:224033471-224034622	K562	blood:	n/a	n/a
4	MAX	chr1:224032986-224034309	K562	blood:	n/a	n/a
5	TAL1	chr1:224033637-224034616	K562	blood:	n/a	n/a
6	TAF1	chr1:224033098-224034370	H1-hESC	embryonic stem cell:	n/a	n/a
7	TCF12	chr1:224032783-224034354	ECC-1	luminal epithelium:	n/a	chr1:224033108-224033118
8	RELA	chr1:224032571-224034424	GM19099	blood:	n/a	chr1:224033222-224033231 chr1:224033222-224033231
9	TAF1	chr1:224033557-224034469	A549	lung:	n/a	n/a
10	MAZ	chr1:224033029-224034297	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:224033225-224034211	HCT-116	colon:	n/a	n/a
12	CEBPB	chr1:224033701-224034248	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr1:224032932-224034356	Hela-S3	cervix:	n/a	n/a
14	CTCF	chr1:224034120-224034270	AG10803	skin:	n/a	n/a
15	POLR2A	chr1:224033173-224034286	A549	lung:	n/a	n/a
16	POLR2A	chr1:224033056-224034571	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr1:224033114-224034559	MCF-7	breast:	n/a	n/a
18	POLR2A	chr1:224033387-224034267	A549	lung:	n/a	n/a
19	EP300	chr1:224032578-224034482	K562	blood:	n/a	chr1:224033856-224033872 chr1:224033857-224033873 chr1:224033318-224033325 chr1:224033230-224033246 chr1:224034068-224034077
20	YY1	chr1:224033690-224034306	HCT-116	colon:	n/a	chr1:224033962-224033973
21	NFIC	chr1:224033782-224034222	HepG2	liver:	n/a	n/a
22	BHLHE40	chr1:224032489-224034345	K562	blood:	n/a	chr1:224033797-224033813 chr1:224033756-224033772
23	POLR2A	chr1:224033133-224034439	HepG2	liver:	n/a	n/a
24	TAF1	chr1:224033542-224034615	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr1:224033114-224034797	Hela-S3	cervix:	n/a	n/a
26	YY1	chr1:224033471-224034566	SK-N-SH_RA	brain:	n/a	chr1:224033962-224033973
27	UBTF	chr1:224032527-224034330	K562	blood:	n/a	n/a
28	POLR2A	chr1:224032904-224034495	HUVEC	blood vessel:	n/a	n/a
29	HNF4G	chr1:224033205-224034207	HepG2	liver:	n/a	n/a
30	POLR2A	chr1:224031692-224034960	K562	blood:	n/a	n/a
31	YY1	chr1:224033659-224034563	H1-hESC	embryonic stem cell:	n/a	chr1:224033962-224033973
32	POLR2A	chr1:224033584-224034253	PANC-1	pancreas:	n/a	n/a
33	SIN3AK20	chr1:224032887-224034309	SK-N-SH	brain:	n/a	n/a
34	TAF1	chr1:224033754-224034293	Hela-S3	cervix:	n/a	n/a
35	TAF1	chr1:224033491-224034364	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:224033397-224034283	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr1:224032950-224034731	K562	blood:	n/a	n/a
38	PML	chr1:224033496-224034280	GM12878	blood:	n/a	n/a
39	POLR2A	chr1:224033111-224034334	GM18951	blood:	n/a	n/a
40	RCOR1	chr1:224033324-224034251	HepG2	liver:	n/a	n/a
41	POLR2A	chr1:224032356-224034896	MCF10A-Er-Src	breast:	n/a	n/a
42	CTCF	chr1:224034140-224034290	GM12871	blood:	n/a	n/a
43	TAF7	chr1:224033468-224034703	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr1:224033343-224034322	PFSK-1	brain:	n/a	n/a
45	POLR2A	chr1:224033341-224034223	GM12878	blood:	n/a	n/a
46	MAX	chr1:224033010-224034642	MCF-7	breast:	n/a	n/a
47	UBTF	chr1:224032199-224034724	K562	blood:	n/a	n/a
48	MYC	chr1:224033719-224034470	H1-hESC	embryonic stem cell:	n/a	n/a
49	HEY1	chr1:224032392-224034875	K562	blood:	n/a	chr1:224034067-224034082 chr1:224033771-224033786 chr1:224033801-224033816 chr1:224033664-224033679 chr1:224033765-224033780
50	CREB1	chr1:224031515-224034709	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:223897551..223903480-chr1:224031634..224036730,7	K562	blood:
2	chr1:223945592..223947499-chr1:224033865..224036173,2	MCF-7	breast:
3	chr1:224033539..224034226-chr8:141522052..141522690,2	HCT-116	colon:
4	chr1:223989156..223991507-chr1:224032637..224036039,3	MCF-7	breast:
5	chr1:224031495..224036851-chr1:224037356..224045519,10	MCF-7	breast:
6	chr1:223877159..223879114-chr1:224033630..224035286,2	MCF-7	breast:
7	chr1:223957411..223959662-chr1:224032167..224034658,2	MCF-7	breast:
8	chr1:224001116..224004491-chr1:224031166..224035522,4	K562	blood:
9	chr1:224011114..224014049-chr1:224032766..224036091,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CAPN2-3	chr1:224033846-224034645	NONHSAT009748

Variant related genes	Relation type
TP53BP2	TF binding region
ENSG00000143514	Chromatin interaction
ENSG00000227621	Chromatin interaction
ENSG00000212398	Chromatin interaction
ENSG00000162909	Chromatin interaction
ENSG00000104472	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs12022914	0.98[ASN][1000 genomes]
rs12022920	0.98[ASN][1000 genomes]
rs12024059	0.98[ASN][1000 genomes]
rs12025911	0.88[ASN][1000 genomes]
rs12026548	0.93[ASN][1000 genomes]
rs12027762	0.88[ASN][1000 genomes]
rs12028843	0.98[ASN][1000 genomes]
rs12029400	0.85[ASN][1000 genomes]
rs12031089	0.85[ASN][1000 genomes]
rs12031127	0.85[ASN][1000 genomes]
rs12031539	0.85[ASN][1000 genomes]
rs12031859	0.98[ASN][1000 genomes]
rs12032205	0.85[ASN][1000 genomes]
rs12032254	0.85[ASN][1000 genomes]
rs12032570	0.85[ASN][1000 genomes]
rs12033388	0.85[ASN][1000 genomes]
rs12033399	0.85[ASN][1000 genomes]
rs12033405	0.85[ASN][1000 genomes]
rs12034120	1.00[ASN][1000 genomes]
rs12034364	0.85[ASN][1000 genomes]
rs12034534	0.85[ASN][1000 genomes]
rs12034737	0.85[ASN][1000 genomes]
rs12034914	1.00[ASN][1000 genomes]
rs12035506	0.90[ASN][1000 genomes]
rs12036390	0.85[ASN][1000 genomes]
rs12036636	0.85[ASN][1000 genomes]
rs12036693	0.85[ASN][1000 genomes]
rs12038665	0.98[ASN][1000 genomes]
rs12038706	1.00[ASN][1000 genomes]
rs12039721	1.00[ASN][1000 genomes]
rs12040996	1.00[ASN][1000 genomes]
rs12043790	0.93[ASN][1000 genomes]
rs12044358	0.93[ASN][1000 genomes]
rs12044652	1.00[ASN][1000 genomes]
rs12044659	1.00[ASN][1000 genomes]
rs12046297	0.85[ASN][1000 genomes]
rs12047342	1.00[ASN][1000 genomes]
rs12047952	0.88[ASN][1000 genomes]
rs1542507	0.93[ASN][1000 genomes]
rs16842259	0.98[ASN][1000 genomes]
rs1981168	0.85[ASN][1000 genomes]
rs1981169	0.85[ASN][1000 genomes]
rs1981170	0.85[ASN][1000 genomes]
rs28370095	0.91[ASN][1000 genomes]
rs28370112	0.91[ASN][1000 genomes]
rs28370115	0.90[ASN][1000 genomes]
rs28370160	0.95[ASN][1000 genomes]
rs28370166	0.93[ASN][1000 genomes]
rs28370174	0.93[ASN][1000 genomes]
rs28370177	0.93[ASN][1000 genomes]
rs28370178	0.93[ASN][1000 genomes]
rs3754088	0.91[ASN][1000 genomes]
rs3767710	0.93[ASN][1000 genomes]
rs3767712	0.86[ASN][1000 genomes]
rs3767713	0.91[ASN][1000 genomes]
rs3820474	0.93[ASN][1000 genomes]
rs3820481	0.91[ASN][1000 genomes]
rs60681980	0.88[ASN][1000 genomes]
rs61437308	0.98[ASN][1000 genomes]
rs747811	0.93[ASN][1000 genomes]
rs7538151	0.91[ASN][1000 genomes]
rs9804140	0.91[ASN][1000 genomes]
rs9970756	0.90[ASN][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	esv3361888	chr1:223725597-224114846	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1007380	chr1:223834380-224042190	Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv535310	chr1:223834380-224042190	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	esv34082	chr1:223851018-224144509	Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv1008800	chr1:223904653-224061032	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	esv2757772	chr1:223935220-224363163	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	esv2759000	chr1:223935220-224363163	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	esv3347515	chr1:224032154-224034902	Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 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	chr1:224030400-224034400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:224030600-224034600	Active TSS	Aorta	Aorta
3	chr1:224031600-224034400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:224031600-224034400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:224031600-224034400	Active TSS	NHLF	lung
6	chr1:224031600-224034600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr1:224031600-224034800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr1:224031600-224034800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:224031600-224034800	Active TSS	Right Ventricle	heart
10	chr1:224031800-224034400	Active TSS	H1 Cell Line	embryonic stem cell
11	chr1:224031800-224034400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:224031800-224034400	Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr1:224031800-224034400	Active TSS	Duodenum Smooth Muscle	Duodenum
14	chr1:224031800-224034400	Active TSS	Fetal Thymus	thymus
15	chr1:224031800-224034400	Active TSS	Left Ventricle	heart
16	chr1:224031800-224034600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr1:224031800-224034600	Active TSS	Esophagus	oesophagus
18	chr1:224032000-224034400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr1:224032000-224034400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:224032000-224034400	Active TSS	Brain Angular Gyrus	brain
21	chr1:224032000-224034400	Active TSS	Colonic Mucosa	Colon
22	chr1:224032000-224034400	Active TSS	Fetal Intestine Large	intestine
23	chr1:224032000-224034400	Active TSS	Fetal Intestine Small	intestine
24	chr1:224032000-224034400	Active TSS	Fetal Stomach	stomach
25	chr1:224032000-224034400	Active TSS	Rectal Mucosa Donor 29	rectum
26	chr1:224032000-224034400	Active TSS	HSMM	muscle
27	chr1:224032000-224034400	Active TSS	HSMMtube	muscle
28	chr1:224032000-224034600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:224032000-224034600	Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr1:224032000-224034600	Active TSS	Brain Substantia Nigra	brain
31	chr1:224032000-224034600	Active TSS	Ovary	ovary
32	chr1:224032000-224034800	Active TSS	Psoas Muscle	Psoas
33	chr1:224032200-224034400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:224032200-224034400	Active TSS	iPS-18 Cell Line	embryonic stem cell
35	chr1:224032200-224034400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr1:224032200-224034400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:224032200-224034400	Active TSS	Brain Anterior Caudate	brain
38	chr1:224032200-224034400	Active TSS	Brain Cingulate Gyrus	brain
39	chr1:224032200-224034400	Active TSS	Fetal Muscle Trunk	muscle
40	chr1:224032200-224034400	Active TSS	K562	blood
41	chr1:224032200-224034600	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr1:224032200-224034600	Active TSS	Fetal Kidney	kidney
43	chr1:224032200-224034600	Active TSS	Skeletal Muscle Male	skeletal muscle
44	chr1:224032200-224034800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr1:224032200-224034800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr1:224032200-224034800	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr1:224032200-224035000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr1:224032400-224034400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr1:224032400-224034400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr1:224032400-224034400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell

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