Variant report

Variant	rs12563308
Chromosome Location	chr1:63069711-63069712
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:63062723..63066181-chr1:63069299..63072097,3	K562	blood:

Variant related genes	Relation type
ENSG00000132855	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10493323	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs10493325	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MKK][hapmap]
rs1168050	1.00[CHB][hapmap]
rs1168121	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12023489	1.00[JPT][hapmap]
rs12062275	1.00[CHB][hapmap]
rs12563863	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12565895	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12566265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1408480	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17123615	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[EUR][1000 genomes]
rs17123688	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17123694	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17123705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17123712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123721	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123725	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123740	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17123743	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2016736	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34898550	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36157139	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3737890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];1.00[EUR][1000 genomes]
rs55709519	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56094630	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56193814	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56792530	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57022388	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59505425	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59662235	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59816054	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60339595	1.00[EUR][1000 genomes]
rs610248	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs61308091	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61501887	1.00[EUR][1000 genomes]
rs74076653	1.00[EUR][1000 genomes]
rs74076654	1.00[EUR][1000 genomes]
rs74076668	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74076670	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74076686	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74076689	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74076691	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74076695	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs74076699	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74076907	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74076909	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs74078610	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74078643	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74078661	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9436224	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1817371	chr1:62901935-63129697	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv1014376	chr1:62976472-63181359	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1011203	chr1:63047046-63081879	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv870559	chr1:63057136-63113719	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1000988	chr1:63061791-63107526	Enhancers Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:63007200-63096200	Weak transcription	HUVEC	blood vessel
2	chr1:63010800-63078400	Weak transcription	A549	lung
3	chr1:63036800-63113600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:63038400-63087600	Weak transcription	NHEK	skin
5	chr1:63038400-63095600	Weak transcription	Brain Germinal Matrix	brain
6	chr1:63038600-63083000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr1:63039200-63095200	Weak transcription	Ovary	ovary
8	chr1:63041000-63095200	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:63041000-63095600	Weak transcription	Fetal Stomach	stomach
10	chr1:63042200-63083600	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:63044000-63076000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:63047600-63077000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:63050600-63083800	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:63051800-63075800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:63051800-63077000	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:63051800-63083400	Weak transcription	Fetal Lung	lung
17	chr1:63051800-63096000	Weak transcription	Left Ventricle	heart
18	chr1:63052400-63083800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr1:63052600-63077200	Weak transcription	HSMM	muscle
20	chr1:63052600-63084400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr1:63054800-63079800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:63054800-63087600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:63057000-63082800	Weak transcription	Brain Anterior Caudate	brain
24	chr1:63057000-63083800	Weak transcription	Adipose Nuclei	Adipose
25	chr1:63060600-63076600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:63062800-63077000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:63063200-63076600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr1:63063200-63085000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:63063600-63076200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:63064600-63074000	Weak transcription	Fetal Intestine Large	intestine
31	chr1:63065200-63079000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr1:63065400-63087800	Weak transcription	Stomach Mucosa	stomach
33	chr1:63066800-63070400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:63066800-63112200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr1:63067000-63070200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:63067600-63077600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:63067800-63070400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr1:63067800-63079400	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr1:63068000-63070400	Strong transcription	NHDF-Ad	bronchial
40	chr1:63068000-63079400	Weak transcription	Osteobl	bone
41	chr1:63068200-63069800	Strong transcription	Liver	Liver
42	chr1:63068200-63074000	Weak transcription	HepG2	liver
43	chr1:63068400-63095200	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:63069000-63076600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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