Variant report

Variant	rs2283789
Chromosome Location	chr22:21944478-21944479
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:21944212..21947141-chr22:21982751..21985738,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161179	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1034329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11089620	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11089629	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11089637	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12158299	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12168958	0.83[AMR][1000 genomes]
rs12169001	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12484550	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs131656	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs131658	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs131659	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs131660	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs131664	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs131665	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140489	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140490	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140491	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140492	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140496	0.95[ASN][1000 genomes]
rs140498	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs140499	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1811069	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs181359	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs181360	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs181361	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs181363	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs181366	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070512	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2256609	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2266959	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2266961	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2266963	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2266964	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283790	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2298428	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2298429	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2876971	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3747093	0.91[ASN][1000 genomes]
rs4821104	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4821108	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4821112	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4821114	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4821116	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4821124	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4821130	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5749485	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749493	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749495	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5749502	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5754100	0.82[EUR][1000 genomes]
rs5754166	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5754177	0.83[AMR][1000 genomes]
rs5754217	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754234	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5754238	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754295	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754323	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754344	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5754352	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5754422	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754426	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754467	0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59391722	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5994638	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5998509	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5998576	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5998599	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5998619	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5998644	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5998672	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66534072	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs710177	0.89[ASN][1000 genomes]
rs73166619	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73166622	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73166630	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73166632	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs738127	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs738128	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7444	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7445	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8137950	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8139079	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs861857	0.88[ASN][1000 genomes]
rs878825	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9619386	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9621715	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1815888	chr22:21486890-21947822	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv1065490	chr22:21567219-21949226	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv1056096	chr22:21567219-21951562	Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
4	esv1797475	chr22:21683210-21950089	Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	esv1816994	chr22:21683210-21950089	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
6	esv1824349	chr22:21683210-21950089	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	esv1826188	chr22:21683210-21950089	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
8	esv1851345	chr22:21683210-21950089	Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv428386	chr22:21683210-21950089	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv914458	chr22:21747678-22070489	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	387 gene(s)	inside rSNPs	diseases
11	nsv834145	chr22:21775069-21950089	Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
12	nsv482690	chr22:21807513-22016791	Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
13	nsv1064360	chr22:21809185-21951562	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
14	esv1823866	chr22:21928916-22131125	Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	374 gene(s)	inside rSNPs	diseases
15	nsv948603	chr22:21928916-22601814	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	422 gene(s)	inside rSNPs	diseases
16	nsv948902	chr22:21928916-22657900	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	426 gene(s)	inside rSNPs	diseases
17	nsv1063962	chr22:21939722-22934593	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases
18	nsv1058617	chr22:21939922-22934454	Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	477 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2283789	CCDC116	cis	lung	GTEx
rs2283789	UBE2L3	Cis_1M	lymphoblastoid	RTeQTL
rs2283789	CCDC116	cis	Artery Tibial	GTEx
rs2283789	UBE2L3	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:21924400-21947400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr22:21925600-21946800	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr22:21925800-21946800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr22:21928800-21945600	Weak transcription	Brain Germinal Matrix	brain
5	chr22:21929000-21945000	Weak transcription	HMEC	breast
6	chr22:21929000-21947000	Weak transcription	HUVEC	blood vessel
7	chr22:21932000-21945200	Weak transcription	A549	lung
8	chr22:21933000-21946800	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr22:21933200-21945400	Weak transcription	Colonic Mucosa	Colon
10	chr22:21933400-21948000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr22:21933800-21946200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr22:21934600-21944800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr22:21934600-21945200	Weak transcription	Fetal Intestine Large	intestine
14	chr22:21934600-21945400	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr22:21936000-21948400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr22:21937400-21945200	Weak transcription	Aorta	Aorta
17	chr22:21937400-21946000	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr22:21937600-21947400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr22:21937800-21945000	Weak transcription	Fetal Lung	lung
20	chr22:21937800-21965400	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr22:21938000-21947200	Weak transcription	Fetal Kidney	kidney
22	chr22:21938200-21945000	Weak transcription	Fetal Heart	heart
23	chr22:21939000-21954000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr22:21939600-21983200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr22:21940200-21945000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr22:21940200-21945400	Weak transcription	Primary T cells from cord blood	blood
27	chr22:21941200-21945200	Enhancers	Primary B cells from peripheral blood	blood
28	chr22:21941200-21946000	Enhancers	Primary B cells from cord blood	blood
29	chr22:21941800-21946600	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr22:21942000-21944600	Enhancers	Placenta	Placenta
31	chr22:21942200-21945200	Weak transcription	Fetal Muscle Trunk	muscle
32	chr22:21942200-21945400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr22:21942200-21947200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr22:21942400-21945000	Weak transcription	Esophagus	oesophagus
35	chr22:21942400-21945000	Weak transcription	Psoas Muscle	Psoas
36	chr22:21942400-21945000	Weak transcription	Right Ventricle	heart
37	chr22:21942400-21945200	Weak transcription	Lung	lung
38	chr22:21942400-21947800	Weak transcription	Fetal Brain Male	brain
39	chr22:21942600-21945000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr22:21942600-21945000	Weak transcription	Brain Anterior Caudate	brain
41	chr22:21942600-21945000	Weak transcription	Fetal Stomach	stomach
42	chr22:21942600-21945000	Weak transcription	NHDF-Ad	bronchial
43	chr22:21942600-21945200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr22:21942600-21945200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr22:21942600-21945200	Weak transcription	Stomach Mucosa	stomach
46	chr22:21942600-21945400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr22:21942600-21945600	Weak transcription	Fetal Brain Female	brain
48	chr22:21942600-21946800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr22:21942600-21947000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr22:21942600-21960800	Weak transcription	Small Intestine	intestine

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