Variant report

Variant	rs8139079
Chromosome Location	chr22:21971632-21971633
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	chr22:21960769..21962604-chr22:21970592..21972163,2	MCF-7	breast:
2	chr22:21949000..21951172-chr22:21970571..21974664,3	MCF-7	breast:

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1034329	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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];0.97[ASN][1000 genomes]
rs11089637	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12158299	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12168958	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12169001	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[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];0.92[ASN][1000 genomes]
rs131658	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs131659	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs131660	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs131664	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs131665	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140489	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140490	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140491	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140492	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140496	0.90[ASN][1000 genomes]
rs140498	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs140499	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1811069	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs181359	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs181360	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs181361	0.90[EUR][1000 genomes]
rs181363	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs181366	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2070512	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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];0.97[ASN][1000 genomes]
rs2283789	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283790	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[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	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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];0.97[ASN][1000 genomes]
rs4821112	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5749485	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5749493	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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];0.94[ASN][1000 genomes]
rs5754234	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5754238	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5754295	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5754323	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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];1.00[ASN][1000 genomes]
rs5754422	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs5754426	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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];0.97[ASN][1000 genomes]
rs5998509	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs5998576	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs5998599	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs5998619	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs5998644	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs5998672	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66534072	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs710177	0.94[ASN][1000 genomes]
rs73166619	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs73166622	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73166630	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73166632	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs738127	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs738128	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7444	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7445	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8137950	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[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	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9621715	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs8139079	CCDC116	cis	lung	GTEx
rs8139079	UBE2L3	Cis_1M	lymphoblastoid	RTeQTL
rs8139079	CCDC116	cis	Artery Tibial	GTEx

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	chr22:21961600-21973600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr22:21962200-21973000	Weak transcription	Psoas Muscle	Psoas
10	chr22:21963600-21978800	Strong transcription	Fetal Thymus	thymus
11	chr22:21964400-21971800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr22:21965200-21974200	Strong transcription	Fetal Intestine Small	intestine
13	chr22:21966000-21973200	Weak transcription	Fetal Kidney	kidney
14	chr22:21966000-21973600	Weak transcription	Esophagus	oesophagus
15	chr22:21966000-21974800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr22:21966400-21976400	Weak transcription	Brain Angular Gyrus	brain
17	chr22:21966400-21976600	Weak transcription	Fetal Lung	lung
18	chr22:21966400-21982800	Weak transcription	Small Intestine	intestine
19	chr22:21966600-21973600	Weak transcription	NHLF	lung
20	chr22:21966600-21974200	Weak transcription	Fetal Heart	heart
21	chr22:21966600-21974400	Weak transcription	Brain Substantia Nigra	brain
22	chr22:21966800-21973600	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr22:21966800-21976200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr22:21967000-21976200	Weak transcription	NHDF-Ad	bronchial
25	chr22:21967400-21976400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr22:21968200-21980600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr22:21968400-21974800	Weak transcription	Fetal Brain Female	brain
28	chr22:21968400-21976400	Weak transcription	Ovary	ovary
29	chr22:21968400-21976600	Weak transcription	Colon Smooth Muscle	Colon
30	chr22:21968400-21977200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr22:21968600-21972600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr22:21968600-21972600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr22:21968600-21973000	Weak transcription	Spleen	Spleen
34	chr22:21968600-21973200	Weak transcription	Brain Germinal Matrix	brain
35	chr22:21968600-21973600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr22:21968600-21973600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr22:21968600-21973600	Weak transcription	Gastric	stomach
38	chr22:21968600-21973600	Weak transcription	Right Atrium	heart
39	chr22:21968600-21974800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr22:21968600-21975000	Weak transcription	Brain Cingulate Gyrus	brain
41	chr22:21968600-21977600	Weak transcription	Aorta	Aorta
42	chr22:21968600-21981000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr22:21968800-21973200	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr22:21969000-21972600	Weak transcription	Fetal Muscle Leg	muscle
45	chr22:21969000-21973000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr22:21969000-21973200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr22:21969000-21973600	Weak transcription	Thymus	Thymus
48	chr22:21969000-21974600	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr22:21969000-21974600	Weak transcription	Rectal Mucosa Donor 31	rectum
50	chr22:21969000-21974800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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