Variant report

Variant	rs5754387
Chromosome Location	chr22:21974703-21974704
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:21968813..21971522-chr22:21971879..21975067,3	MCF-7	breast:
2	chr22:21973254..21975110-chr22:22291149..22292766,2	K562	blood:

Variant related genes	Relation type
ENSG00000224086	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1034329	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11089629	1.00[CEU][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs11089637	0.84[CEU][hapmap];0.95[GIH][hapmap];0.90[TSI][hapmap]
rs12158299	0.91[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs12484550	1.00[CEU][hapmap]
rs131665	0.91[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs140488	0.89[ASW][hapmap]
rs140489	1.00[CEU][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs140491	0.91[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs140492	1.00[CEU][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs140498	0.91[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap]
rs140499	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs181359	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs181360	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2070512	1.00[CEU][hapmap];0.98[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs2266959	1.00[CEU][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap]
rs2266961	1.00[CEU][hapmap]
rs2266963	1.00[CEU][hapmap]
rs2283790	0.91[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs2298428	1.00[CEU][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap]
rs2298429	1.00[CEU][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs4820091	0.84[CEU][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.90[TSI][hapmap]
rs4821108	1.00[CEU][hapmap];1.00[YRI][hapmap]
rs4821112	0.91[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs4821116	1.00[CEU][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap]
rs4821124	1.00[CEU][hapmap];0.96[MEX][hapmap];0.90[TSI][hapmap]
rs4821130	1.00[ASW][hapmap];0.92[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs5749502	1.00[CEU][hapmap]
rs5754217	1.00[CEU][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs5754295	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs5754352	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs5754467	0.81[ASW][hapmap];0.92[CEU][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.81[YRI][hapmap]
rs5998599	1.00[CEU][hapmap]
rs5998619	1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs5998672	1.00[CEU][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs738127	0.91[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap]
rs7444	1.00[CEU][hapmap];0.89[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs878825	1.00[CEU][hapmap];0.98[GIH][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap]
rs9621715	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs5754387	CCDC116	cis	Esophagus Muscularis	GTEx
rs5754387	UBE2L3	cis	multi-tissue	Pritchard
rs5754387	CCDC116	cis	lung	GTEx
rs5754387	KIAA1666	cis	multi-tissue	Pritchard
rs5754387	CCDC116	cis	Artery Tibial	GTEx
rs5754387	UBE2L3	cis	lymphoblastoid	seeQTL

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	chr22:21946400-21980200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr22:21949200-21976600	Weak transcription	Fetal Brain Male	brain
4	chr22:21950000-21978600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr22:21959000-21981200	Strong transcription	Dnd41	blood
6	chr22:21960200-21974800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr22:21960400-21976600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr22:21963600-21978800	Strong transcription	Fetal Thymus	thymus
9	chr22:21966000-21974800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr22:21966400-21976400	Weak transcription	Brain Angular Gyrus	brain
11	chr22:21966400-21976600	Weak transcription	Fetal Lung	lung
12	chr22:21966400-21982800	Weak transcription	Small Intestine	intestine
13	chr22:21966800-21976200	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr22:21967000-21976200	Weak transcription	NHDF-Ad	bronchial
15	chr22:21967400-21976400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr22:21968200-21980600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr22:21968400-21974800	Weak transcription	Fetal Brain Female	brain
18	chr22:21968400-21976400	Weak transcription	Ovary	ovary
19	chr22:21968400-21976600	Weak transcription	Colon Smooth Muscle	Colon
20	chr22:21968400-21977200	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr22:21968600-21974800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr22:21968600-21975000	Weak transcription	Brain Cingulate Gyrus	brain
23	chr22:21968600-21977600	Weak transcription	Aorta	Aorta
24	chr22:21968600-21981000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr22:21969000-21974800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr22:21969000-21975000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr22:21969000-21976200	Weak transcription	HSMM	muscle
28	chr22:21969000-21978800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr22:21969000-21982400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr22:21969000-21983400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr22:21969200-21974800	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr22:21969200-21974800	Weak transcription	NH-A	brain
33	chr22:21969200-21975000	Weak transcription	Brain Anterior Caudate	brain
34	chr22:21969200-21975600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr22:21969200-21976200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr22:21969200-21976400	Weak transcription	Stomach Smooth Muscle	stomach
37	chr22:21969200-21976600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr22:21969200-21977800	Weak transcription	HSMMtube	muscle
39	chr22:21969200-21978200	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr22:21969200-21981000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr22:21970000-21974800	Weak transcription	Liver	Liver
42	chr22:21970200-21974800	Weak transcription	Lung	lung
43	chr22:21970200-21976600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr22:21970200-21977000	Weak transcription	Colonic Mucosa	Colon
45	chr22:21970400-21974800	Weak transcription	Adipose Nuclei	Adipose
46	chr22:21970400-21974800	Weak transcription	Brain Hippocampus Middle	brain
47	chr22:21970400-21975000	Weak transcription	A549	lung
48	chr22:21970400-21975600	Weak transcription	Osteobl	bone
49	chr22:21970400-21976800	Weak transcription	HUVEC	blood vessel
50	chr22:21970400-21977200	Weak transcription	Hela-S3	cervix

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