Variant report

Variant	rs12562109
Chromosome Location	chr1:223934171-223934172
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	chr1:223932764-223934266	U87	brain:	n/a	n/a
2	POLR2A	chr1:223932764-223934269	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:223886106..223889532-chr1:223933715..223936535,3	K562	blood:

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

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10503144	0.81[EUR][1000 genomes]
rs10915702	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915707	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915715	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1153965	0.88[EUR][1000 genomes]
rs12059128	0.83[EUR][1000 genomes]
rs12059770	0.83[EUR][1000 genomes]
rs12060361	0.83[EUR][1000 genomes]
rs12066704	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066829	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066831	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069561	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070057	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12080250	0.86[EUR][1000 genomes]
rs12088254	0.85[EUR][1000 genomes]
rs12091841	0.83[EUR][1000 genomes]
rs1222134	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1222138	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222140	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1222141	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1222142	0.85[EUR][1000 genomes]
rs12563291	0.94[EUR][1000 genomes]
rs12563477	0.86[EUR][1000 genomes]
rs12563637	0.92[EUR][1000 genomes]
rs12563713	0.93[EUR][1000 genomes]
rs12565967	0.83[EUR][1000 genomes]
rs12566817	0.81[EUR][1000 genomes]
rs16842162	0.86[EUR][1000 genomes]
rs16842229	0.83[EUR][1000 genomes]
rs16842257	0.81[EUR][1000 genomes]
rs17597	0.94[EUR][1000 genomes]
rs17598	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28370043	0.80[EUR][1000 genomes]
rs28370069	0.90[EUR][1000 genomes]
rs28370073	0.83[EUR][1000 genomes]
rs28370074	0.83[EUR][1000 genomes]
rs28370088	0.83[EUR][1000 genomes]
rs28370159	0.82[EUR][1000 genomes]
rs28370170	0.86[EUR][1000 genomes]
rs34683843	0.83[EUR][1000 genomes]
rs36032024	0.81[EUR][1000 genomes]
rs3738373	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738374	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738375	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767716	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3767717	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3767718	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3885657	0.83[EUR][1000 genomes]
rs59248553	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59275322	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61823580	0.81[EUR][1000 genomes]
rs61823581	0.81[EUR][1000 genomes]
rs61823583	0.81[EUR][1000 genomes]
rs61823585	0.81[EUR][1000 genomes]
rs61823587	0.81[EUR][1000 genomes]
rs61823591	0.81[EUR][1000 genomes]
rs61824003	0.86[EUR][1000 genomes]
rs61824005	0.85[EUR][1000 genomes]
rs61824008	0.83[EUR][1000 genomes]
rs6604724	0.83[EUR][1000 genomes]
rs6604727	0.81[EUR][1000 genomes]
rs6658954	0.81[EUR][1000 genomes]
rs6665485	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674541	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6674846	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682412	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6682964	0.83[EUR][1000 genomes]
rs6685557	0.83[EUR][1000 genomes]
rs6691315	0.83[EUR][1000 genomes]
rs6694960	0.83[EUR][1000 genomes]
rs7331	0.86[EUR][1000 genomes]
rs751609	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530328	0.83[EUR][1000 genomes]
rs7533551	0.83[EUR][1000 genomes]
rs7555226	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs898876	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs898877	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[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	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

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223915400-223936200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:223919200-223935600	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:223919200-223936200	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr1:223921200-223936000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:223921600-223936600	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:223921800-223935600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:223921800-223936000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:223922200-223934600	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:223922200-223935600	Weak transcription	Fetal Brain Male	brain
10	chr1:223922800-223934800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:223925200-223934600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr1:223925400-223934800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:223927800-223935400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
14	chr1:223928000-223935400	Weak transcription	Small Intestine	intestine
15	chr1:223928000-223935600	Weak transcription	Right Atrium	heart
16	chr1:223928000-223936400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:223928400-223936200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:223929000-223934800	Weak transcription	Fetal Kidney	kidney
19	chr1:223929800-223935200	Weak transcription	Fetal Heart	heart
20	chr1:223930000-223935000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr1:223930200-223934800	Strong transcription	Fetal Stomach	stomach
22	chr1:223930200-223935000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr1:223930200-223935400	Strong transcription	Fetal Intestine Small	intestine
24	chr1:223930200-223935600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr1:223930400-223935200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:223930400-223935400	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr1:223930400-223935800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:223930400-223935800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:223930400-223936000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:223930600-223934800	Strong transcription	NHEK	skin
31	chr1:223930600-223935000	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr1:223930600-223935200	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr1:223930600-223935200	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr1:223930600-223935400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr1:223930600-223935400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr1:223930600-223935400	Strong transcription	Fetal Lung	lung
37	chr1:223930600-223935400	Strong transcription	Rectal Mucosa Donor 29	rectum
38	chr1:223930600-223935600	Strong transcription	Fetal Intestine Large	intestine
39	chr1:223930600-223935800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr1:223930600-223936200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr1:223930800-223935200	Strong transcription	Primary T cells from cord blood	blood
42	chr1:223930800-223935400	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr1:223930800-223935600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr1:223930800-223935600	Strong transcription	Colonic Mucosa	Colon
45	chr1:223931000-223934800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:223931000-223935000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr1:223931200-223935400	Strong transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:223931200-223954800	Strong transcription	HMEC	breast
49	chr1:223931400-223935200	Strong transcription	Brain Anterior Caudate	brain
50	chr1:223931400-223935800	Strong transcription	Rectal Smooth Muscle	rectum

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