Variant report

Variant	rs12233589
Chromosome Location	chr3:160089896-160089897
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:160089127..160092102-chr3:160166087..160168050,2	K562	blood:
2	chr3:160089762..160091914-chr3:160096661..160098564,2	K562	blood:
3	chr3:160087287..160090245-chr3:160100813..160102924,2	K562	blood:

Variant related genes	Relation type
ENSG00000213186	Chromatin interaction
ENSG00000068885	Chromatin interaction

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10513550	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs10513552	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11920289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275150	0.81[ASW][hapmap];0.91[LWK][hapmap];0.91[YRI][hapmap];0.80[AFR][1000 genomes]
rs2275153	0.95[EUR][1000 genomes]
rs2305401	1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs2305406	0.95[EUR][1000 genomes]
rs33999879	0.95[EUR][1000 genomes]
rs3736627	1.00[CEU][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes]
rs3773371	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs3806629	0.88[GIH][hapmap];0.93[TSI][hapmap]
rs41272959	0.91[EUR][1000 genomes]
rs55815116	0.95[EUR][1000 genomes]
rs56119270	0.98[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56124988	0.86[EUR][1000 genomes]
rs56150006	0.98[EUR][1000 genomes]
rs56401539	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57030267	0.98[EUR][1000 genomes]
rs57050097	0.89[EUR][1000 genomes]
rs57277659	0.89[EUR][1000 genomes]
rs57285344	0.98[EUR][1000 genomes]
rs57555307	0.89[EUR][1000 genomes]
rs57843971	0.82[ASN][1000 genomes]
rs58627305	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58654032	0.98[EUR][1000 genomes]
rs58776572	0.93[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58915028	0.98[EUR][1000 genomes]
rs59695030	0.82[EUR][1000 genomes]
rs59799252	0.91[EUR][1000 genomes]
rs60066272	0.86[EUR][1000 genomes]
rs60153357	0.98[EUR][1000 genomes]
rs60607858	0.83[AFR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60914777	0.98[EUR][1000 genomes]
rs61066536	0.98[EUR][1000 genomes]
rs62272176	0.95[EUR][1000 genomes]
rs62272179	0.98[EUR][1000 genomes]
rs62272180	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62272181	0.98[EUR][1000 genomes]
rs62272185	0.98[EUR][1000 genomes]
rs62272187	0.98[EUR][1000 genomes]
rs62272188	0.98[EUR][1000 genomes]
rs62272190	0.98[EUR][1000 genomes]
rs62272191	0.98[EUR][1000 genomes]
rs62272193	0.98[EUR][1000 genomes]
rs62272196	0.98[EUR][1000 genomes]
rs62272197	0.98[EUR][1000 genomes]
rs62272198	0.98[EUR][1000 genomes]
rs62272205	0.82[EUR][1000 genomes]
rs62272207	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62272231	0.98[EUR][1000 genomes]
rs62272236	0.95[EUR][1000 genomes]
rs62272237	0.95[EUR][1000 genomes]
rs62272245	0.91[EUR][1000 genomes]
rs62272247	0.91[EUR][1000 genomes]
rs62272249	0.89[EUR][1000 genomes]
rs62272251	0.86[EUR][1000 genomes]
rs62272254	0.89[EUR][1000 genomes]
rs62272255	0.89[EUR][1000 genomes]
rs62272256	0.89[EUR][1000 genomes]
rs62272257	0.89[EUR][1000 genomes]
rs62272258	0.89[EUR][1000 genomes]
rs62272259	0.89[EUR][1000 genomes]
rs62272780	0.86[EUR][1000 genomes]
rs62272781	0.86[EUR][1000 genomes]
rs62272783	0.86[EUR][1000 genomes]
rs62272785	0.86[EUR][1000 genomes]
rs62272787	0.86[EUR][1000 genomes]
rs62272788	0.86[EUR][1000 genomes]
rs62272790	0.82[EUR][1000 genomes]
rs62272793	0.82[EUR][1000 genomes]
rs62272799	0.81[EUR][1000 genomes]
rs66769612	0.98[EUR][1000 genomes]
rs66850724	0.91[EUR][1000 genomes]
rs68069205	0.91[EUR][1000 genomes]
rs6808628	0.81[ASW][hapmap];0.91[LWK][hapmap];0.91[YRI][hapmap]
rs73154587	0.93[EUR][1000 genomes]
rs73155914	0.89[EUR][1000 genomes]
rs7614701	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618017	0.98[EUR][1000 genomes]
rs7645798	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648832	0.89[EUR][1000 genomes]
rs9637414	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	esv1801474	chr3:160012843-160153305	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	206 gene(s)	inside rSNPs	diseases
7	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
8	esv1795255	chr3:160089896-160153305	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	205 gene(s)	inside rSNPs	diseases
9	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160049400-160090600	Weak transcription	NH-A	brain
2	chr3:160054400-160091600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:160055200-160103400	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:160056200-160091000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:160056400-160098000	Weak transcription	Aorta	Aorta
6	chr3:160056600-160091600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:160061400-160109600	Weak transcription	Fetal Heart	heart
8	chr3:160063400-160094000	Weak transcription	Fetal Brain Female	brain
9	chr3:160065000-160091600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:160066400-160099200	Weak transcription	NHEK	skin
11	chr3:160067800-160097800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:160068600-160096000	Weak transcription	Gastric	stomach
13	chr3:160068800-160094000	Weak transcription	Adipose Nuclei	Adipose
14	chr3:160068800-160094000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr3:160069000-160115200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:160070400-160092400	Weak transcription	HMEC	breast
17	chr3:160071000-160091000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:160071400-160098200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:160071400-160102000	Weak transcription	Small Intestine	intestine
20	chr3:160071600-160099400	Weak transcription	Placenta	Placenta
21	chr3:160071800-160091800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:160071800-160092000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:160072000-160096400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:160072600-160096200	Weak transcription	HepG2	liver
25	chr3:160072800-160091200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr3:160073000-160091600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:160073000-160092600	Weak transcription	Fetal Kidney	kidney
28	chr3:160073200-160091600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:160073200-160097200	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr3:160073400-160090800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr3:160073400-160099200	Weak transcription	HSMMtube	muscle
32	chr3:160073800-160090000	Weak transcription	A549	lung
33	chr3:160073800-160090600	Weak transcription	Fetal Intestine Large	intestine
34	chr3:160073800-160091000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:160073800-160091200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:160073800-160092400	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr3:160073800-160092800	Weak transcription	Brain Anterior Caudate	brain
38	chr3:160073800-160108400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr3:160074000-160090600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr3:160074000-160091000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:160074200-160090400	Weak transcription	NHLF	lung
42	chr3:160074200-160091600	Weak transcription	Brain Germinal Matrix	brain
43	chr3:160074400-160090000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:160074600-160091400	Weak transcription	Left Ventricle	heart
45	chr3:160074800-160101400	Weak transcription	Brain Angular Gyrus	brain
46	chr3:160075000-160094400	Weak transcription	Colon Smooth Muscle	Colon
47	chr3:160075200-160090800	Weak transcription	Ovary	ovary
48	chr3:160075600-160094000	Weak transcription	HSMM	muscle
49	chr3:160076200-160116200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr3:160076400-160091400	Weak transcription	Primary B cells from peripheral blood	blood

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