Variant report

Variant	rs56072942
Chromosome Location	chr5:68477812-68477813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:68463301..68465130-chr5:68476296..68477877,2	MCF-7	breast:
2	chr5:68477360..68479387-chr5:68480784..68482809,2	MCF-7	breast:
3	chr5:68473378..68475599-chr5:68475846..68477931,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC125-1	chr5:68477525-68477829	XLOC_004864

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10454825	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10515100	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10940208	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1128761	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12188874	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12189395	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16875380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271735	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271763	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17271912	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17331590	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2069432	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28616082	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3846484	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3966728	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41392244	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56101109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56667192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57047253	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58176819	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58725071	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59497209	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61626775	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61699334	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61743885	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs66525615	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66595384	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67275234	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67548500	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67693452	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67821207	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67980996	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867050	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6890817	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767813	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767816	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767820	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767822	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767833	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs72767837	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767849	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72767855	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767860	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767861	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767863	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767864	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72767865	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7709090	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7714908	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734513	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7736312	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	esv3378789	chr5:68438275-68540725	Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
4	esv3445512	chr5:68472245-68495835	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56072942	CCDC125	cis	lung	GTEx

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68463800-68484400	Weak transcription	Adipose Nuclei	Adipose
2	chr5:68463800-68484400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr5:68463800-68484400	Weak transcription	Colon Smooth Muscle	Colon
4	chr5:68464000-68478000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:68464000-68478800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr5:68464000-68484400	Weak transcription	Pancreas	Pancrea
7	chr5:68464000-68484600	Weak transcription	Right Atrium	heart
8	chr5:68464200-68484600	Weak transcription	Left Ventricle	heart
9	chr5:68464400-68479000	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr5:68464400-68484400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr5:68464600-68484400	Weak transcription	HSMMtube	muscle
12	chr5:68466800-68484400	Weak transcription	Fetal Heart	heart
13	chr5:68468000-68484400	Weak transcription	Brain Hippocampus Middle	brain
14	chr5:68468000-68484400	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr5:68468400-68484400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr5:68470600-68484200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr5:68471200-68484400	Weak transcription	Brain Anterior Caudate	brain
18	chr5:68471200-68484400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:68471200-68484600	Weak transcription	Primary T cells from cord blood	blood
20	chr5:68471200-68484600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr5:68471400-68484400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:68471400-68484400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr5:68471400-68484600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr5:68471400-68484600	Weak transcription	Liver	Liver
25	chr5:68471400-68484600	Weak transcription	Brain Substantia Nigra	brain
26	chr5:68471400-68484600	Weak transcription	Spleen	Spleen
27	chr5:68471600-68484200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr5:68471600-68484400	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr5:68471600-68484400	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr5:68471600-68484600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr5:68471600-68484800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr5:68472000-68484400	Weak transcription	Fetal Intestine Large	intestine
33	chr5:68472000-68484600	Weak transcription	Ovary	ovary
34	chr5:68472200-68479200	Weak transcription	Fetal Kidney	kidney
35	chr5:68472200-68479600	Weak transcription	Brain Angular Gyrus	brain
36	chr5:68472200-68484400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr5:68472200-68484400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr5:68472200-68484400	Weak transcription	NHLF	lung
39	chr5:68472200-68484600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr5:68472400-68484400	Weak transcription	Fetal Intestine Small	intestine
41	chr5:68472400-68484600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr5:68472800-68484400	Weak transcription	Fetal Stomach	stomach
43	chr5:68473400-68484200	Weak transcription	Placenta	Placenta
44	chr5:68473400-68484400	Weak transcription	GM12878-XiMat	blood
45	chr5:68473400-68484600	Weak transcription	Thymus	Thymus
46	chr5:68473600-68484400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr5:68473600-68484400	Weak transcription	Fetal Muscle Leg	muscle
48	chr5:68473600-68484400	Weak transcription	HUVEC	blood vessel
49	chr5:68473600-68484600	Weak transcription	Primary B cells from cord blood	blood
50	chr5:68473800-68481800	Weak transcription	K562	blood

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