Variant report

Variant	rs11920289
Chromosome Location	chr3:160096355-160096356
allele	A/C
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	GATA3	chr3:160096046-160097373	SK-N-SH	brain:	n/a	n/a
2	NR3C1	chr3:160096140-160096483	A549	lung:	n/a	n/a
3	NR3C1	chr3:160096265-160096406	A549	lung:	n/a	n/a
4	GATA3	chr3:160096319-160097449	SK-N-SH	brain:	n/a	n/a
5	NFIC	chr3:160096321-160097052	SK-N-SH	brain:	n/a	n/a
6	NR3C1	chr3:160096144-160096452	A549	lung:	n/a	n/a
7	NR3C1	chr3:160096226-160096442	A549	lung:	n/a	n/a
8	GATA1	chr3:160096104-160096517	PBDE	blood:	n/a	n/a

Variant related genes	Relation type
IFT80	TF binding region

Extended variants
information (count: 88 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10513550	0.98[EUR][1000 genomes]
rs12233589	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275150	0.80[AFR][1000 genomes]
rs2275153	0.95[EUR][1000 genomes]
rs2305401	0.86[EUR][1000 genomes]
rs2305406	0.95[EUR][1000 genomes]
rs33999879	0.95[EUR][1000 genomes]
rs3736627	0.82[EUR][1000 genomes]
rs3773371	0.91[EUR][1000 genomes]
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]
rs73154587	0.93[EUR][1000 genomes]
rs73155914	0.89[EUR][1000 genomes]
rs7614701	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	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:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160055200-160103400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:160056400-160098000	Weak transcription	Aorta	Aorta
3	chr3:160061400-160109600	Weak transcription	Fetal Heart	heart
4	chr3:160066400-160099200	Weak transcription	NHEK	skin
5	chr3:160067800-160097800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr3:160069000-160115200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr3:160071400-160098200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr3:160071400-160102000	Weak transcription	Small Intestine	intestine
9	chr3:160071600-160099400	Weak transcription	Placenta	Placenta
10	chr3:160072000-160096400	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr3:160073200-160097200	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr3:160073400-160099200	Weak transcription	HSMMtube	muscle
13	chr3:160073800-160108400	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:160074800-160101400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:160076200-160116200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:160077400-160098200	Weak transcription	Lung	lung
17	chr3:160081200-160102200	Weak transcription	HUVEC	blood vessel
18	chr3:160081800-160100000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:160083000-160097000	Weak transcription	Right Ventricle	heart
20	chr3:160083400-160113000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:160083600-160098000	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:160083800-160097400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr3:160083800-160108200	Weak transcription	GM12878-XiMat	blood
24	chr3:160083800-160116000	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr3:160084000-160104000	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:160087600-160098000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr3:160088200-160099800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr3:160088800-160101400	Weak transcription	Hela-S3	cervix
29	chr3:160088800-160108600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr3:160088800-160108600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr3:160088800-160116200	Weak transcription	Primary B cells from cord blood	blood
32	chr3:160088800-160116200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr3:160089000-160098000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr3:160089000-160104000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr3:160090400-160096400	Weak transcription	Colonic Mucosa	Colon
36	chr3:160091600-160105800	Weak transcription	Ovary	ovary
37	chr3:160092000-160097200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:160092000-160113200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:160092200-160097800	Weak transcription	Thymus	Thymus
40	chr3:160092200-160098200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr3:160092200-160100400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:160092200-160103200	Weak transcription	K562	blood
43	chr3:160092200-160116000	Weak transcription	Fetal Stomach	stomach
44	chr3:160092200-160116200	Weak transcription	Fetal Intestine Small	intestine
45	chr3:160092200-160116600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:160092400-160097800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:160092600-160097800	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr3:160093000-160096800	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr3:160093000-160102800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:160093000-160113000	Weak transcription	NHLF	lung

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