Variant report

Variant	rs350122
Chromosome Location	chr5:68474945-68474946
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:68470570-68475878	K562	blood:	n/a	n/a
2	POLR2A	chr5:68474132-68476112	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:68473506-68475287	U87	brain:	n/a	n/a
4	POLR2A	chr5:68474851-68475453	U87	brain:	n/a	n/a
5	POLR2A	chr5:68474102-68475542	PANC-1	pancreas:	n/a	n/a
6	POLR2A	chr5:68474890-68475236	HepG2	liver:	n/a	n/a
7	POLR2A	chr5:68474911-68475417	U87	brain:	n/a	n/a
8	POLR2A	chr5:68474162-68475198	PBDE	blood:	n/a	n/a
9	POLR2A	chr5:68473517-68476577	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr5:68474036-68475798	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr5:68473512-68475346	U87	brain:	n/a	n/a
12	POLR2A	chr5:68474358-68475051	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr5:68474887-68475859	PANC-1	pancreas:	n/a	n/a
14	POLR2A	chr5:68474232-68475685	K562	blood:	n/a	n/a
15	POLR2A	chr5:68473968-68475378	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr5:68474818-68475240	ECC-1	luminal epithelium:	n/a	n/a
17	POLR2A	chr5:68474324-68475983	SK-N-MC	brain:	n/a	n/a
18	POLR2A	chr5:68474270-68475815	MCF-7	breast:	n/a	n/a
19	POLR2A	chr5:68474241-68475825	Hela-S3	cervix:	n/a	n/a
20	BCL3	chr5:68474895-68475340	A549	lung:	n/a	n/a
21	POLR2A	chr5:68474830-68475133	PFSK-1	brain:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:68473378..68475599-chr5:68475846..68477931,2	MCF-7	breast:
2	chr5:68473528..68475096-chr5:68513422..68515325,2	K562	blood:
3	chr5:68473756..68475838-chr5:68491178..68492966,2	K562	blood:
4	chr5:68472735..68477267-chr5:68482092..68486946,8	MCF-7	breast:
5	chr5:68337794..68340461-chr5:68472784..68475376,2	K562	blood:
6	chr5:68462470..68464043-chr5:68472593..68475057,3	MCF-7	breast:
7	chr5:68469522..68472583-chr5:68472918..68475943,4	MCF-7	breast:
8	chr5:68469019..68470647-chr5:68473560..68475120,2	MCF-7	breast:
9	chr5:68471354..68475028-chr5:68512445..68515750,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000238334	TF binding region
ENSG00000153044	Chromatin interaction
ENSG00000250237	Chromatin interaction
ENSG00000238334	Chromatin interaction
ENSG00000134056	Chromatin interaction
ENSG00000134057	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10063757	0.89[EUR][1000 genomes]
rs10940209	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10940210	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11748974	0.81[ASN][1000 genomes]
rs13175606	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs151589	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs163444	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs164709	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs164715	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs164789	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1650779	0.87[ASN][1000 genomes]
rs171212	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs184747	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1976103	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2130757	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2171148	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2172056	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2242350	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2291519	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2291520	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2450230	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2450246	0.85[ASN][1000 genomes]
rs28602964	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28768211	0.88[EUR][1000 genomes]
rs2930945	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2930949	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2930951	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2932767	0.85[ASN][1000 genomes]
rs2932772	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932773	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932774	0.81[EUR][1000 genomes]
rs2932775	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932776	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2932782	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2972361	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972366	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972377	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2972378	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2972381	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972386	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972387	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2972388	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34893396	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs350104	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs350105	0.80[ASN][1000 genomes]
rs350106	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs350107	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350109	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs350115	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs350116	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs350123	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs351424	0.88[ASN][1000 genomes]
rs35308484	0.90[EUR][1000 genomes]
rs353656	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs379106	0.88[ASN][1000 genomes]
rs386640	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3934528	0.84[ASN][1000 genomes]
rs4077460	0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs419902	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs426392	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4266362	0.83[ASN][1000 genomes]
rs4362903	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4421064	0.84[ASN][1000 genomes]
rs4541612	0.82[ASN][1000 genomes]
rs4629549	0.85[ASN][1000 genomes]
rs488498	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs603029	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62373164	0.84[ASN][1000 genomes]
rs6450026	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6450027	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs651076	0.86[ASN][1000 genomes]
rs676012	0.91[EUR][1000 genomes]
rs676879	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6866993	0.85[ASN][1000 genomes]
rs6876783	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs693725	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7733556	0.85[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs350122	CCDC125	cis	lung	GTEx
rs350122	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs350122	CCDC125	cis	Muscle Skeletal	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

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	chr5:68464000-68475000	Weak transcription	Colonic Mucosa	Colon
5	chr5:68464000-68476200	Weak transcription	Stomach Mucosa	stomach
6	chr5:68464000-68478000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr5:68464000-68478800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr5:68464000-68484400	Weak transcription	Pancreas	Pancrea
9	chr5:68464000-68484600	Weak transcription	Right Atrium	heart
10	chr5:68464200-68484600	Weak transcription	Left Ventricle	heart
11	chr5:68464400-68479000	Weak transcription	Primary T helper cells PMA-I stimulated	--
12	chr5:68464400-68484400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr5:68464600-68484400	Weak transcription	HSMMtube	muscle
14	chr5:68466800-68484400	Weak transcription	Fetal Heart	heart
15	chr5:68468000-68484400	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:68468000-68484400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr5:68468400-68484400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:68470600-68484200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr5:68471200-68476600	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr5:68471200-68477200	Weak transcription	HepG2	liver
21	chr5:68471200-68484400	Weak transcription	Brain Anterior Caudate	brain
22	chr5:68471200-68484400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr5:68471200-68484600	Weak transcription	Primary T cells from cord blood	blood
24	chr5:68471200-68484600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr5:68471400-68476200	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr5:68471400-68477800	Weak transcription	Gastric	stomach
27	chr5:68471400-68484400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr5:68471400-68484400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr5:68471400-68484600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr5:68471400-68484600	Weak transcription	Liver	Liver
31	chr5:68471400-68484600	Weak transcription	Brain Substantia Nigra	brain
32	chr5:68471400-68484600	Weak transcription	Spleen	Spleen
33	chr5:68471600-68476000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr5:68471600-68476000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:68471600-68476400	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr5:68471600-68476600	Weak transcription	Fetal Brain Female	brain
37	chr5:68471600-68484200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr5:68471600-68484400	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr5:68471600-68484400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr5:68471600-68484600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:68471600-68484800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr5:68472000-68484400	Weak transcription	Fetal Intestine Large	intestine
43	chr5:68472000-68484600	Weak transcription	Ovary	ovary
44	chr5:68472200-68479200	Weak transcription	Fetal Kidney	kidney
45	chr5:68472200-68479600	Weak transcription	Brain Angular Gyrus	brain
46	chr5:68472200-68484400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:68472200-68484400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr5:68472200-68484400	Weak transcription	NHLF	lung
49	chr5:68472200-68484600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr5:68472400-68484400	Weak transcription	Fetal Intestine Small	intestine

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