Variant report

Variant	rs5754426
Chromosome Location	chr22:21980638-21980639
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:21978725..21981306-chr5:114359469..114360989,2	K562	blood:
2	chr13:91999778..92002355-chr22:21977509..21981284,3	K562	blood:
3	chr22:21979187..21986650-chr22:21993296..22001177,21	MCF-7	breast:
4	chr17:57920551..57922161-chr22:21979706..21982473,2	K562	blood:
5	chr2:197034205..197037096-chr22:21979390..21982259,2	K562	blood:
6	chr22:21979975..21982573-chr22:22086401..22089371,3	K562	blood:
7	chr22:21979602..21983329-chr22:22291845..22295097,4	K562	blood:
8	chr22:21805758..21807437-chr22:21977909..21980793,2	K562	blood:
9	chr22:21979247..21980981-chr5:118401357..118402877,3	K562	blood:
10	chr22:21979671..21985739-chr22:22220007..22225195,6	K562	blood:
11	chr22:21979643..21982522-chr22:22334996..22337250,2	K562	blood:
12	chr17:56756357..56758489-chr22:21978206..21981191,3	K562	blood:
13	chr22:21979236..21981171-chr22:22220521..22222509,2	K562	blood:
14	chr22:21921267..21924236-chr22:21978074..21981837,4	MCF-7	breast:
15	chr22:21908736..21910357-chr22:21980107..21982427,2	K562	blood:
16	chr18:66743023..66744541-chr22:21979665..21981555,2	K562	blood:
17	chr22:21799659..21804135-chr22:21977326..21984068,6	K562	blood:
18	chr22:21931758..21934175-chr22:21978835..21981370,2	MCF-7	breast:
19	chr22:21979310..21981506-chrX:31657956..31659478,2	K562	blood:
20	chr22:21978899..21981344-chr22:22856790..22858574,2	K562	blood:
21	chr22:21980146..21981915-chr6:27116049..27117685,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000128228	Chromatin interaction
ENSG00000200997	Chromatin interaction
ENSG00000215417	Chromatin interaction
ENSG00000100038	Chromatin interaction
ENSG00000100030	Chromatin interaction
ENSG00000273342	Chromatin interaction
ENSG00000185651	Chromatin interaction
ENSG00000224086	Chromatin interaction
ENSG00000100034	Chromatin interaction
ENSG00000081320	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1034329	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11089620	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11089629	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11089637	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12158299	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12168958	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12169001	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12484550	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs131656	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs131658	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs131659	0.82[EUR][1000 genomes]
rs131660	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs131664	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs131665	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140489	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140490	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140491	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140492	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140496	0.89[ASN][1000 genomes]
rs140498	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs140499	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1811069	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs181359	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs181360	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs181361	0.90[EUR][1000 genomes]
rs181363	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs181366	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2070512	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2256609	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2266959	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2266961	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2266963	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2266964	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2283789	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2283790	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2298428	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2298429	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2876971	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3747093	0.97[ASN][1000 genomes]
rs4821104	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4821108	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4821112	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4821114	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4821116	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4821124	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4821130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5749485	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5749493	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5749495	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5749502	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754100	0.81[EUR][1000 genomes]
rs5754166	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5754177	0.82[AMR][1000 genomes]
rs5754217	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5754234	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754238	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5754295	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5754323	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754344	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5754352	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5754422	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754467	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59391722	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs5994638	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5998509	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5998576	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5998599	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5998619	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5998644	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5998672	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66534072	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs710177	0.94[ASN][1000 genomes]
rs73166619	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73166622	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73166630	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73166632	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs738127	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs738128	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7444	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7445	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8137950	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8139079	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs861857	0.94[ASN][1000 genomes]
rs878825	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9619386	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9621715	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
8	nsv529694	chr22:21957411-22905068	Enhancers Genic enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	474 gene(s)	inside rSNPs	diseases
9	nsv914464	chr22:21964761-22039863	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	367 gene(s)	inside rSNPs	diseases
10	nsv914465	chr22:21964761-22055280	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' 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	368 gene(s)	inside rSNPs	diseases
11	nsv914466	chr22:21964761-22057273	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
12	nsv531797	chr22:21977700-22959729	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	476 gene(s)	inside rSNPs	diseases
13	esv3328497	chr22:21980213-21980674	Strong transcription Weak transcription Genic enhancers Enhancers	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs5754426	CCDC116	cis	Artery Tibial	GTEx
rs5754426	UBE2L3	cis	multi-tissue	Pritchard
rs5754426	CCDC116	cis	lung	GTEx
rs5754426	UBE2L3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:21939600-21983200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr22:21959000-21981200	Strong transcription	Dnd41	blood
3	chr22:21966400-21982800	Weak transcription	Small Intestine	intestine
4	chr22:21968600-21981000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr22:21969000-21982400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr22:21969000-21983400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr22:21969200-21981000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr22:21970600-21980800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr22:21972600-21981000	Strong transcription	Primary T cells from cord blood	blood
10	chr22:21973600-21982400	Strong transcription	Thymus	Thymus
11	chr22:21974000-21983400	Weak transcription	Fetal Kidney	kidney
12	chr22:21974400-21981000	Strong transcription	GM12878-XiMat	blood
13	chr22:21974800-21982400	Strong transcription	Fetal Intestine Small	intestine
14	chr22:21975400-21981600	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr22:21975600-21981200	Weak transcription	Rectal Smooth Muscle	rectum
16	chr22:21976800-21983200	Weak transcription	Ovary	ovary
17	chr22:21976800-21983200	Weak transcription	HSMM	muscle
18	chr22:21977000-21981600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr22:21977000-21983200	Weak transcription	NHDF-Ad	bronchial
20	chr22:21977600-21981600	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr22:21977600-21982800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr22:21977600-21983200	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr22:21977800-21982400	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr22:21977800-21982600	Weak transcription	NH-A	brain
25	chr22:21977800-21983000	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr22:21978000-21980800	Genic enhancers	K562	blood
27	chr22:21978000-21981200	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr22:21978000-21981800	Weak transcription	Hela-S3	cervix
29	chr22:21978000-21982200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr22:21978000-21982200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr22:21978000-21982200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr22:21978000-21983200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr22:21978000-21983200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr22:21978200-21980800	Enhancers	Pancreas	Pancrea
35	chr22:21978200-21981400	Weak transcription	HMEC	breast
36	chr22:21978200-21982400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr22:21978200-21983200	Genic enhancers	Primary T cells fromperipheralblood	blood
38	chr22:21978400-21982000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr22:21978400-21982400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr22:21978400-21982400	Weak transcription	HepG2	liver
41	chr22:21978400-21982600	Weak transcription	Colonic Mucosa	Colon
42	chr22:21978400-21983200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr22:21978400-21983200	Weak transcription	Osteobl	bone
44	chr22:21978400-21983400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr22:21978400-21983400	Weak transcription	Fetal Lung	lung
46	chr22:21978600-21980800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr22:21978600-21981400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr22:21978600-21982600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr22:21978600-21982600	Weak transcription	HUVEC	blood vessel
50	chr22:21978800-21981000	Enhancers	Primary monocytes fromperipheralblood	blood

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