Variant report

Variant	rs5998644
Chromosome Location	chr22:21953288-21953289
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	chr22:21951983..21954689-chr22:21981334..21984467,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000161179	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1034329	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11089620	0.85[EUR][1000 genomes]
rs11089629	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11089637	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12158299	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12168958	0.81[EUR][1000 genomes]
rs12169001	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12484550	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs131656	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131658	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs131659	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs131660	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs131664	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs131665	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs140489	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs140490	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs140491	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs140492	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs140496	0.93[ASN][1000 genomes]
rs140498	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs140499	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1811069	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs181359	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs181360	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs181361	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs181363	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs181366	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2070512	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2256609	0.84[EUR][1000 genomes]
rs2266959	0.85[EUR][1000 genomes]
rs2266961	0.85[EUR][1000 genomes]
rs2266963	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2266964	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283789	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2283790	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298428	0.89[EUR][1000 genomes]
rs2298429	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2876971	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3747093	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4821104	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4821108	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4821112	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4821114	0.91[EUR][1000 genomes]
rs4821116	0.92[EUR][1000 genomes]
rs4821124	0.93[EUR][1000 genomes]
rs4821130	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5749485	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749493	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5749495	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5749502	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5754100	0.80[EUR][1000 genomes]
rs5754166	0.85[EUR][1000 genomes]
rs5754217	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754234	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5754238	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5754295	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754323	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5754344	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754352	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754422	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754426	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754467	0.94[ASN][1000 genomes]
rs59391722	0.85[EUR][1000 genomes]
rs5994638	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998509	0.84[EUR][1000 genomes]
rs5998576	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs5998599	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5998619	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5998672	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66534072	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs710177	0.92[ASN][1000 genomes]
rs73166619	0.85[EUR][1000 genomes]
rs73166622	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73166630	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73166632	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs738127	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs738128	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7444	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7445	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8137950	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8139079	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs861857	0.91[ASN][1000 genomes]
rs878825	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9619386	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9621715	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]

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	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
2	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
3	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
4	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
5	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
6	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
7	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
rs5998644	UBE2L3	Cis_1M	lymphoblastoid	RTeQTL
rs5998644	CCDC116	cis	Artery Tibial	GTEx
rs5998644	CCDC116	cis	lung	GTEx
rs5998644	UBE2L3	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:21937800-21965400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:21939000-21954000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr22:21939600-21983200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr22:21942600-21960800	Weak transcription	Small Intestine	intestine
5	chr22:21943400-21963600	Strong transcription	Fetal Intestine Small	intestine
6	chr22:21943800-21954200	Strong transcription	Dnd41	blood
7	chr22:21945000-21955200	Strong transcription	Fetal Stomach	stomach
8	chr22:21945800-21954200	Strong transcription	GM12878-XiMat	blood
9	chr22:21946000-21954000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr22:21946200-21954000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr22:21946200-21954600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr22:21946400-21960200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr22:21946400-21980200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr22:21946600-21953800	Strong transcription	HSMM	muscle
15	chr22:21946800-21954000	Strong transcription	Primary B cells from peripheral blood	blood
16	chr22:21946800-21954200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr22:21947200-21954000	Strong transcription	Fetal Muscle Leg	muscle
18	chr22:21948800-21953400	Weak transcription	Brain Angular Gyrus	brain
19	chr22:21948800-21953600	Weak transcription	Psoas Muscle	Psoas
20	chr22:21948800-21965200	Weak transcription	Fetal Kidney	kidney
21	chr22:21949200-21960400	Weak transcription	Fetal Heart	heart
22	chr22:21949200-21976600	Weak transcription	Fetal Brain Male	brain
23	chr22:21949400-21960200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr22:21949400-21965400	Weak transcription	Hela-S3	cervix
25	chr22:21949600-21956400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr22:21949600-21965200	Weak transcription	Colon Smooth Muscle	Colon
27	chr22:21949800-21953400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr22:21949800-21953400	Weak transcription	Gastric	stomach
29	chr22:21949800-21956400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr22:21949800-21956400	Weak transcription	Ovary	ovary
31	chr22:21949800-21956600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr22:21949800-21956600	Weak transcription	HSMMtube	muscle
33	chr22:21949800-21960200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr22:21949800-21960400	Weak transcription	Colonic Mucosa	Colon
35	chr22:21949800-21965200	Weak transcription	Brain Anterior Caudate	brain
36	chr22:21949800-21965400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr22:21949800-21965400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr22:21949800-21968800	Weak transcription	Stomach Mucosa	stomach
39	chr22:21950000-21953400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr22:21950000-21953400	Weak transcription	Left Ventricle	heart
41	chr22:21950000-21953400	Weak transcription	Pancreas	Pancrea
42	chr22:21950000-21956400	Weak transcription	Primary B cells from cord blood	blood
43	chr22:21950000-21956400	Weak transcription	Lung	lung
44	chr22:21950000-21956800	Weak transcription	Right Atrium	heart
45	chr22:21950000-21960000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr22:21950000-21960400	Weak transcription	Brain Germinal Matrix	brain
47	chr22:21950000-21965200	Weak transcription	H9 Cell Line	embryonic stem cell
48	chr22:21950000-21965200	Weak transcription	Rectal Smooth Muscle	rectum
49	chr22:21950000-21965400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr22:21950000-21978600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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