Variant report

Variant	rs67548500
Chromosome Location	chr5:68474235-68474236
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:30)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:30 , 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	JUND	chr5:68474216-68474652	HCT-116	colon:	n/a	n/a
3	POLR2A	chr5:68473803-68474689	HepG2	liver:	n/a	n/a
4	CCNT2	chr5:68474223-68474428	K562	blood:	n/a	n/a
5	POLR2A	chr5:68474132-68476112	HepG2	liver:	n/a	n/a
6	POLR2A	chr5:68473506-68475287	U87	brain:	n/a	n/a
7	POLR2A	chr5:68473961-68474714	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr5:68474102-68475542	PANC-1	pancreas:	n/a	n/a
9	POLR2A	chr5:68474210-68474778	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr5:68474187-68474832	U87	brain:	n/a	n/a
11	POLR2A	chr5:68474157-68474751	A549	lung:	n/a	n/a
12	POLR2A	chr5:68474201-68474573	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr5:68474181-68474636	GM12878	blood:	n/a	n/a
14	CHD2	chr5:68474133-68474601	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr5:68474183-68474922	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr5:68474162-68475198	PBDE	blood:	n/a	n/a
17	POLR2A	chr5:68474189-68474279	GM12878	blood:	n/a	n/a
18	POLR2A	chr5:68474027-68474726	PFSK-1	brain:	n/a	n/a
19	POLR2A	chr5:68474158-68474754	K562	blood:	n/a	n/a
20	POLR2A	chr5:68474122-68474816	HCT-116	colon:	n/a	n/a
21	POLR2A	chr5:68473517-68476577	MCF10A-Er-Src	breast:	n/a	n/a
22	POLR2A	chr5:68474204-68474858	PANC-1	pancreas:	n/a	n/a
23	POLR2A	chr5:68474187-68474814	U87	brain:	n/a	n/a
24	POLR2A	chr5:68474036-68475798	SK-N-SH	brain:	n/a	n/a
25	POLR2A	chr5:68473901-68474675	PFSK-1	brain:	n/a	n/a
26	POLR2A	chr5:68473512-68475346	U87	brain:	n/a	n/a
27	BCL3	chr5:68474141-68474873	A549	lung:	n/a	n/a
28	POLR2A	chr5:68474232-68475685	K562	blood:	n/a	n/a
29	POLR2A	chr5:68474049-68474763	HepG2	liver:	n/a	n/a
30	POLR2A	chr5:68473968-68475378	MCF10A-Er-Src	breast:	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
ENSG00000250237	Chromatin interaction
ENSG00000153044	Chromatin interaction
ENSG00000134057	Chromatin interaction
ENSG00000238334	Chromatin interaction
ENSG00000134056	Chromatin interaction

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]
rs56072942	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
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
rs67548500	CCDC125	cis	lung	GTEx

Chromatin state (count:110 , 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	chr5:68464200-68474600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:68464200-68484600	Weak transcription	Left Ventricle	heart
12	chr5:68464400-68479000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr5:68464400-68484400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr5:68464600-68484400	Weak transcription	HSMMtube	muscle
15	chr5:68464800-68474400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:68464800-68474400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:68464800-68474600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:68464800-68474600	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr5:68464800-68474600	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr5:68464800-68474600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr5:68465200-68474600	Strong transcription	H1 Cell Line	embryonic stem cell
22	chr5:68465400-68474400	Strong transcription	HSMM	muscle
23	chr5:68465400-68474800	Strong transcription	NHEK	skin
24	chr5:68465600-68474800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:68466200-68474400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr5:68466200-68474400	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr5:68466200-68474600	Strong transcription	Cortex derived primary cultured neurospheres	brain
28	chr5:68466400-68474600	Strong transcription	Primary neutrophils fromperipheralblood	blood
29	chr5:68466600-68474600	Strong transcription	A549	lung
30	chr5:68466800-68484400	Weak transcription	Fetal Heart	heart
31	chr5:68467800-68474400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:68467800-68474400	Strong transcription	HMEC	breast
33	chr5:68467800-68474600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:68468000-68484400	Weak transcription	Brain Hippocampus Middle	brain
35	chr5:68468000-68484400	Weak transcription	Skeletal Muscle Female	skeletal muscle
36	chr5:68468400-68474600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr5:68468400-68484400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr5:68469200-68474400	Strong transcription	Dnd41	blood
39	chr5:68469200-68474600	Strong transcription	NHDF-Ad	bronchial
40	chr5:68470600-68484200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr5:68471200-68474600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr5:68471200-68476600	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr5:68471200-68477200	Weak transcription	HepG2	liver
44	chr5:68471200-68484400	Weak transcription	Brain Anterior Caudate	brain
45	chr5:68471200-68484400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr5:68471200-68484600	Weak transcription	Primary T cells from cord blood	blood
47	chr5:68471200-68484600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr5:68471400-68474400	Strong transcription	Fetal Lung	lung
49	chr5:68471400-68476200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr5:68471400-68477800	Weak transcription	Gastric	stomach

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