Variant report

Variant	rs12563713
Chromosome Location	chr1:223937520-223937521
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SMC3	chr1:223936280-223937855	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr1:223937406-223937595	HUVEC	blood vessel:	n/a	n/a
3	CTCF	chr1:223937503-223937550	Kidney_OC	kidney:	n/a	n/a
4	CTCF	chr1:223936566-223937572	SK-N-SH	brain:	n/a	n/a
5	CTCF	chr1:223936390-223937743	A549	lung:	n/a	n/a
6	POLR2A	chr1:223934506-223937545	K562	blood:	n/a	n/a
7	CTCF	chr1:223937380-223937530	GM12864	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:223885511..223886611-chr1:223936562..223937549,9	K562	blood:
2	chr1:223925259..223927259-chr1:223937310..223938830,2	K562	blood:
3	chr1:223936854..223938919-chr1:223960180..223962303,2	K562	blood:
4	chr1:223924785..223927259-chr1:223936900..223938830,2	K562	blood:
5	chr1:223937050..223939736-chr1:223946719..223949161,2	K562	blood:
6	chr1:223884441..223887114-chr1:223935723..223937532,2	MCF-7	breast:
7	chr1:223897059..223902247-chr1:223935403..223939761,6	K562	blood:
8	chr1:223931041..223933395-chr1:223937050..223938620,2	K562	blood:
9	chr1:223885662..223886577-chr1:223936613..223937522,3	MCF-7	breast:
10	chr1:223936472..223939236-chr1:224031329..224033727,2	K562	blood:
11	chr1:223915826..223918177-chr1:223937169..223939533,2	K562	blood:
12	chr1:223898965..223904523-chr1:223935616..223939096,7	MCF-7	breast:
13	chr1:223884772..223887549-chr1:223936018..223938654,2	MCF-7	breast:
14	chr1:223899274..223906539-chr1:223934896..223938666,15	MCF-7	breast:
15	chr1:223937021..223937991-chr1:223946905..223947482,2	K562	blood:

No data

Variant related genes	Relation type
CAPN2	TF binding region
ENSG00000143514	Chromatin interaction
ENSG00000162909	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10465524	1.00[ASN][1000 genomes]
rs10503144	0.87[EUR][1000 genomes]
rs10915702	0.90[EUR][1000 genomes]
rs10915707	0.93[EUR][1000 genomes]
rs10915715	0.96[EUR][1000 genomes]
rs1153958	0.87[ASN][1000 genomes]
rs1153965	0.89[EUR][1000 genomes]
rs12059128	0.90[EUR][1000 genomes]
rs12059770	0.90[EUR][1000 genomes]
rs12060361	0.90[EUR][1000 genomes]
rs12066704	0.90[EUR][1000 genomes]
rs12066829	0.90[EUR][1000 genomes]
rs12066831	0.90[EUR][1000 genomes]
rs12069561	0.93[EUR][1000 genomes]
rs12070057	0.90[EUR][1000 genomes]
rs12080250	0.93[EUR][1000 genomes]
rs12088254	0.89[EUR][1000 genomes]
rs12091841	0.90[EUR][1000 genomes]
rs1222134	0.93[EUR][1000 genomes]
rs1222138	0.92[EUR][1000 genomes]
rs1222140	0.87[EUR][1000 genomes]
rs1222141	0.87[EUR][1000 genomes]
rs1222142	0.84[EUR][1000 genomes]
rs12562109	0.93[EUR][1000 genomes]
rs12563291	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563477	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12563637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12565967	0.90[EUR][1000 genomes]
rs12566817	0.87[EUR][1000 genomes]
rs16842162	0.93[EUR][1000 genomes]
rs16842229	0.90[EUR][1000 genomes]
rs16842257	0.87[EUR][1000 genomes]
rs17557525	0.82[EUR][1000 genomes]
rs17557623	0.82[EUR][1000 genomes]
rs17597	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17598	0.93[EUR][1000 genomes]
rs17600	0.93[EUR][1000 genomes]
rs28370026	0.82[EUR][1000 genomes]
rs28370031	0.82[EUR][1000 genomes]
rs28370032	0.82[EUR][1000 genomes]
rs28370043	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370069	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28370073	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370074	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370088	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370159	0.89[EUR][1000 genomes]
rs28370170	0.93[EUR][1000 genomes]
rs34683843	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36032024	0.87[EUR][1000 genomes]
rs3738373	0.93[EUR][1000 genomes]
rs3738374	0.93[EUR][1000 genomes]
rs3738375	0.93[EUR][1000 genomes]
rs3767716	0.94[EUR][1000 genomes]
rs3767717	0.93[EUR][1000 genomes]
rs3767718	0.93[EUR][1000 genomes]
rs3885657	0.90[EUR][1000 genomes]
rs59248553	0.85[EUR][1000 genomes]
rs59275322	0.87[EUR][1000 genomes]
rs61823580	0.87[EUR][1000 genomes]
rs61823581	0.87[EUR][1000 genomes]
rs61823583	0.87[EUR][1000 genomes]
rs61823585	0.87[EUR][1000 genomes]
rs61823587	0.87[EUR][1000 genomes]
rs61823591	0.87[EUR][1000 genomes]
rs61823964	0.93[AMR][1000 genomes]
rs61824003	0.93[EUR][1000 genomes]
rs61824005	0.89[EUR][1000 genomes]
rs61824008	0.90[EUR][1000 genomes]
rs6604724	0.90[EUR][1000 genomes]
rs6604727	0.87[EUR][1000 genomes]
rs6604728	0.86[EUR][1000 genomes]
rs6604729	0.86[EUR][1000 genomes]
rs6658954	0.87[EUR][1000 genomes]
rs6665485	0.94[EUR][1000 genomes]
rs6671245	0.82[EUR][1000 genomes]
rs6674541	0.90[EUR][1000 genomes]
rs6674846	0.90[EUR][1000 genomes]
rs6678365	0.86[EUR][1000 genomes]
rs6682412	0.84[EUR][1000 genomes]
rs6682964	0.90[EUR][1000 genomes]
rs6683052	0.82[EUR][1000 genomes]
rs6685475	0.82[EUR][1000 genomes]
rs6685557	0.90[EUR][1000 genomes]
rs6691315	0.90[EUR][1000 genomes]
rs6693884	0.82[EUR][1000 genomes]
rs6694960	0.90[EUR][1000 genomes]
rs6696053	1.00[ASN][1000 genomes]
rs6700366	0.86[EUR][1000 genomes]
rs7331	0.93[EUR][1000 genomes]
rs751609	0.90[EUR][1000 genomes]
rs7528455	0.86[EUR][1000 genomes]
rs7530328	0.90[EUR][1000 genomes]
rs7533551	0.90[EUR][1000 genomes]
rs7548911	0.87[ASN][1000 genomes]
rs7549063	0.82[EUR][1000 genomes]
rs7555226	0.87[EUR][1000 genomes]
rs898876	0.90[EUR][1000 genomes]
rs898877	0.89[EUR][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	nsv832681	chr1:223698048-224002691	Strong transcription Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv520609	chr1:223931411-223947081	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
8	nsv521758	chr1:223931411-223954080	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
9	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
10	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

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223931200-223954800	Strong transcription	HMEC	breast
2	chr1:223931400-223954400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:223935800-223952600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr1:223936600-223954800	Strong transcription	NHEK	skin
5	chr1:223936800-223937800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr1:223936800-223938200	Weak transcription	Spleen	Spleen
7	chr1:223936800-223942800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:223936800-223947400	Weak transcription	Fetal Brain Male	brain
9	chr1:223936800-223954400	Strong transcription	HSMM	muscle
10	chr1:223937000-223937600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:223937000-223937600	Weak transcription	Brain Substantia Nigra	brain
12	chr1:223937000-223937600	Weak transcription	Placenta	Placenta
13	chr1:223937000-223937600	Weak transcription	Left Ventricle	heart
14	chr1:223937000-223937800	Weak transcription	Primary T cells from cord blood	blood
15	chr1:223937000-223937800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr1:223937000-223937800	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr1:223937000-223938000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:223937000-223938000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:223937000-223938000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr1:223937000-223938200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr1:223937000-223938200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr1:223937000-223938200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:223937000-223938200	Weak transcription	Brain Angular Gyrus	brain
24	chr1:223937000-223938200	Weak transcription	Ovary	ovary
25	chr1:223937000-223938200	Weak transcription	Pancreas	Pancrea
26	chr1:223937000-223938200	Weak transcription	Psoas Muscle	Psoas
27	chr1:223937000-223938400	Weak transcription	Aorta	Aorta
28	chr1:223937000-223938400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr1:223937000-223938400	Weak transcription	HepG2	liver
30	chr1:223937000-223939000	Weak transcription	Liver	Liver
31	chr1:223937000-223939000	Weak transcription	Fetal Thymus	thymus
32	chr1:223937000-223939400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:223937000-223939600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr1:223937000-223940000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:223937000-223940200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr1:223937000-223940200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr1:223937000-223940200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr1:223937000-223940200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr1:223937000-223940200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr1:223937000-223940200	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr1:223937000-223940400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:223937000-223940600	Weak transcription	Small Intestine	intestine
43	chr1:223937000-223940800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr1:223937000-223943200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:223937000-223943400	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr1:223937000-223945400	Strong transcription	Hela-S3	cervix
47	chr1:223937000-223947600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr1:223937000-223948000	Strong transcription	Lung	lung
49	chr1:223937000-223948200	Weak transcription	Right Atrium	heart
50	chr1:223937000-223951200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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