Variant report

Variant	rs12566817
Chromosome Location	chr1:224017175-224017176
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	chr1:223999352..224002189-chr1:224016108..224019082,3	K562	blood:
2	chr1:223984174..223985831-chr1:224015824..224018657,2	K562	blood:

Variant related genes	Relation type
ENSG00000143514	Chromatin interaction

Extended variants
information (count: 112 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10465524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.84[TSI][hapmap]
rs10495215	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs10495216	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10495217	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs10503144	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10915707	0.81[EUR][1000 genomes]
rs10915715	0.83[EUR][1000 genomes]
rs1153965	0.90[EUR][1000 genomes]
rs12046297	0.91[EUR][1000 genomes]
rs12059128	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12059770	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12060361	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12066704	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs12069561	0.85[CEU][hapmap];0.88[GIH][hapmap];0.81[EUR][1000 genomes]
rs12080250	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12088254	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs12091841	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1222134	0.81[EUR][1000 genomes]
rs1222138	0.85[CEU][hapmap];0.88[GIH][hapmap]
rs1222141	0.85[CEU][hapmap]
rs12562109	0.81[EUR][1000 genomes]
rs12563291	0.86[EUR][1000 genomes]
rs12563477	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12563637	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[EUR][1000 genomes]
rs12563713	0.87[EUR][1000 genomes]
rs12564557	1.00[ASN][1000 genomes]
rs12565202	1.00[ASN][1000 genomes]
rs12565573	1.00[ASN][1000 genomes]
rs12565967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12568612	0.85[CEU][hapmap]
rs1629836	1.00[CEU][hapmap]
rs16841190	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16842162	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842229	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs16842257	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842326	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16842343	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17556570	0.85[CEU][hapmap]
rs17557288	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17557525	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs17557623	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17597	0.86[EUR][1000 genomes]
rs17598	0.85[CEU][hapmap];0.88[GIH][hapmap];0.81[EUR][1000 genomes]
rs17600	0.81[EUR][1000 genomes]
rs28370069	0.84[EUR][1000 genomes]
rs28370073	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28370074	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28370088	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28370159	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28370170	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34683843	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36032024	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3738373	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs3738374	0.85[CEU][hapmap];0.88[GIH][hapmap];0.81[EUR][1000 genomes]
rs3738375	0.81[EUR][1000 genomes]
rs3767716	0.82[EUR][1000 genomes]
rs3767717	0.81[EUR][1000 genomes]
rs3767718	0.81[EUR][1000 genomes]
rs3885657	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41303996	1.00[ASN][1000 genomes]
rs4653522	0.85[CEU][hapmap]
rs4993742	0.82[CEU][hapmap]
rs58774026	1.00[ASN][1000 genomes]
rs61823580	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61823581	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823583	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823585	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823587	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61823591	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824003	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61824005	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61824008	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604727	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604728	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604729	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6604730	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658954	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6665485	0.82[EUR][1000 genomes]
rs6671245	1.00[CEU][hapmap]
rs6678365	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682964	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6683052	1.00[CEU][hapmap]
rs6685475	1.00[CEU][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6685557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693372	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6693884	0.82[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs6694960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696053	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6696222	1.00[ASN][1000 genomes]
rs6700366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703104	0.85[CEU][hapmap]
rs73116425	1.00[ASN][1000 genomes]
rs73116447	1.00[ASN][1000 genomes]
rs73116451	1.00[ASN][1000 genomes]
rs73116456	1.00[ASN][1000 genomes]
rs7331	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7515821	1.00[ASN][1000 genomes]
rs751609	0.85[CEU][hapmap]
rs7528455	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530328	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7533551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7535882	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549063	1.00[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223960200-224025400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:224002000-224023800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:224002200-224020200	Weak transcription	Placenta	Placenta
4	chr1:224002200-224020200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr1:224007000-224024000	Weak transcription	Fetal Intestine Small	intestine
6	chr1:224007800-224020200	Weak transcription	Stomach Smooth Muscle	stomach
7	chr1:224008000-224019800	Weak transcription	Brain Germinal Matrix	brain
8	chr1:224008200-224019400	Weak transcription	Hela-S3	cervix
9	chr1:224008600-224019400	Weak transcription	A549	lung
10	chr1:224008800-224020200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:224009000-224018800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr1:224009000-224019400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr1:224009000-224019400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr1:224009000-224020400	Weak transcription	Fetal Muscle Leg	muscle
15	chr1:224009200-224019600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr1:224009200-224020400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr1:224009400-224019400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:224009400-224019800	Weak transcription	HSMM	muscle
19	chr1:224009400-224019800	Weak transcription	NHDF-Ad	bronchial
20	chr1:224009400-224020200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr1:224009400-224023800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:224010200-224026400	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr1:224011000-224020200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:224011200-224019400	Weak transcription	NH-A	brain
25	chr1:224011200-224019400	Weak transcription	Osteobl	bone
26	chr1:224011400-224019600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr1:224013400-224017200	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr1:224013800-224019400	Weak transcription	Fetal Lung	lung
29	chr1:224013800-224019400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:224013800-224021600	Weak transcription	Ovary	ovary
31	chr1:224014000-224019400	Weak transcription	Brain Anterior Caudate	brain
32	chr1:224014000-224019400	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:224014000-224019800	Weak transcription	Adipose Nuclei	Adipose
34	chr1:224014000-224020200	Weak transcription	Liver	Liver
35	chr1:224014000-224020200	Weak transcription	Esophagus	oesophagus
36	chr1:224014200-224019400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr1:224014200-224019800	Weak transcription	Primary B cells from peripheral blood	blood
38	chr1:224014200-224019800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:224014200-224020200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr1:224014200-224020200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:224014200-224020400	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:224014200-224021400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr1:224014200-224023400	Weak transcription	Thymus	Thymus
44	chr1:224014200-224023400	Weak transcription	Dnd41	blood
45	chr1:224014200-224024400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr1:224014400-224018000	Enhancers	Primary neutrophils fromperipheralblood	blood
47	chr1:224014400-224020400	Weak transcription	Fetal Thymus	thymus
48	chr1:224014600-224019600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr1:224014600-224019800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:224015000-224017400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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