Variant report

Variant	rs350104
Chromosome Location	chr5:68462438-68462439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EP300	chr5:68462412-68463160	K562	blood:	n/a	chr5:68462897-68462910 chr5:68463056-68463072 chr5:68462750-68462766
2	MTA3	chr5:68462267-68463338	GM12878	blood:	n/a	n/a
3	IRF1	chr5:68462409-68463107	K562	blood:	n/a	chr5:68462411-68462420 chr5:68462821-68462835 chr5:68462560-68462574
4	MAX	chr5:68462338-68463469	ECC-1	luminal epithelium:	n/a	chr5:68462376-68462386 chr5:68462778-68462789 chr5:68462778-68462789 chr5:68462778-68462787
5	CEBPB	chr5:68462391-68463141	GM12878	blood:	n/a	n/a
6	MYBL2	chr5:68462287-68463360	HepG2	liver:	n/a	n/a
7	E2F6	chr5:68462352-68463387	A549	lung:	n/a	chr5:68462761-68462770
8	SIN3AK20	chr5:68462263-68464138	MCF-7	breast:	n/a	n/a
9	MAX	chr5:68462390-68463372	SK-N-SH	brain:	n/a	chr5:68462778-68462789 chr5:68462778-68462789 chr5:68462778-68462787
10	POLR2A	chr5:68462393-68464203	SK-N-MC	brain:	n/a	n/a
11	CREB1	chr5:68462397-68463250	HepG2	liver:	n/a	n/a
12	MAZ	chr5:68462331-68463917	IMR90	lung:	n/a	chr5:68462376-68462386 chr5:68462778-68462789 chr5:68462778-68462789 chr5:68462778-68462787
13	E2F4	chr5:68462256-68463931	MCF10A-Er-Src	breast:	n/a	chr5:68462761-68462770 chr5:68462842-68462853
14	FOXM1	chr5:68462291-68463891	SK-N-SH	brain:	n/a	n/a
15	POLR2A	chr5:68462329-68463669	K562	blood:	n/a	n/a
16	FOXM1	chr5:68462341-68463616	GM12878	blood:	n/a	n/a
17	MXI1	chr5:68462182-68464879	SK-N-SH	brain:	n/a	chr5:68462851-68462866
18	MAX	chr5:68462436-68463385	SK-N-SH	brain:	n/a	chr5:68462778-68462789 chr5:68462778-68462789 chr5:68462778-68462787
19	POLR2A	chr5:68462397-68463542	PANC-1	pancreas:	n/a	n/a
20	GTF2F1	chr5:68462404-68463184	Hela-S3	cervix:	n/a	n/a
21	MAX	chr5:68462301-68463500	HepG2	liver:	n/a	chr5:68462376-68462386 chr5:68462778-68462789 chr5:68462778-68462789 chr5:68462778-68462787
22	POLR2A	chr5:68462407-68463366	GM12878	blood:	n/a	n/a
23	POLR2A	chr5:68462329-68463918	PBDE	blood:	n/a	n/a
24	REST	chr5:68462270-68463249	A549	lung:	n/a	chr5:68463050-68463070 chr5:68463056-68463069 chr5:68462933-68462946 chr5:68463051-68463069
25	HCFC1	chr5:68462189-68463535	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr5:68462407-68463406	SK-N-SH	brain:	n/a	n/a
27	TEAD4	chr5:68462424-68463371	K562	blood:	n/a	n/a
28	UBTF	chr5:68462339-68463737	K562	blood:	n/a	n/a
29	POLR2A	chr5:68462360-68463983	U87	brain:	n/a	n/a
30	RFX5	chr5:68462171-68463315	IMR90	lung:	n/a	n/a
31	MBD4	chr5:68462355-68462943	HepG2	liver:	n/a	n/a
32	POLR2A	chr5:68462435-68463326	K562	blood:	n/a	n/a
33	MAX	chr5:68462374-68463444	ECC-1	luminal epithelium:	n/a	chr5:68462376-68462386 chr5:68462778-68462789 chr5:68462778-68462789 chr5:68462778-68462787
34	FOXM1	chr5:68462354-68463612	ECC-1	luminal epithelium:	n/a	n/a
35	POLR2A	chr5:68461951-68464229	GM12891	blood:	n/a	n/a
36	MYBL2	chr5:68462385-68463534	HepG2	liver:	n/a	n/a
37	POLR2A	chr5:68462302-68463898	HepG2	liver:	n/a	n/a
38	MAX	chr5:68462419-68463316	K562	blood:	n/a	chr5:68462778-68462789 chr5:68462778-68462789 chr5:68462778-68462787
39	IRF1	chr5:68462182-68463270	K562	blood:	n/a	chr5:68462411-68462420 chr5:68462821-68462835 chr5:68462560-68462574
40	USF1	chr5:68462365-68463153	HCT-116	colon:	n/a	chr5:68462745-68462761
41	MAX	chr5:68462332-68463425	K562	blood:	n/a	chr5:68462376-68462386 chr5:68462778-68462789 chr5:68462778-68462789 chr5:68462778-68462787
42	POLR2A	chr5:68462405-68463343	HUVEC	blood vessel:	n/a	n/a
43	MAFK	chr5:68462348-68463189	Hela-S3	cervix:	n/a	n/a
44	POLR2A	chr5:68462360-68463433	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr5:68462406-68463658	MCF-7	breast:	n/a	n/a
46	TEAD4	chr5:68462408-68463193	K562	blood:	n/a	n/a
47	POLR2A	chr5:68462335-68463703	K562	blood:	n/a	n/a
48	POLR2A	chr5:68462413-68463304	HCT-116	colon:	n/a	n/a
49	TCF12	chr5:68462344-68463387	ECC-1	luminal epithelium:	n/a	n/a
50	ZNF384	chr5:68462258-68463146	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:68461458..68463761-chr5:68512888..68515184,2	MCF-7	breast:
2	chr5:68452033..68456569-chr5:68461553..68463610,4	K562	blood:
3	chr5:68461460..68464018-chr5:68483608..68486992,6	MCF-7	breast:
4	chr5:68461677..68464671-chr5:68665186..68667008,2	MCF-7	breast:
5	chr5:68461899..68464283-chr5:68662357..68663862,2	K562	blood:
6	chr5:68461057..68464340-chr5:68513596..68515366,3	K562	blood:
7	chr5:68461424..68464982-chr5:68663773..68666998,5	K562	blood:
8	chr5:68387785..68391337-chr5:68461261..68464730,5	K562	blood:

Variant related genes	Relation type
CCNB1	TF binding region
ENSG00000153044	Chromatin interaction
ENSG00000145740	Chromatin interaction
ENSG00000134056	Chromatin interaction
ENSG00000085231	Chromatin interaction
ENSG00000265968	Chromatin interaction
ENSG00000152942	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10045526	0.83[ASN][1000 genomes]
rs10063757	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10063969	0.97[ASN][1000 genomes]
rs10940209	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10940210	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12513817	0.87[ASN][1000 genomes]
rs13175606	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13362324	0.87[ASN][1000 genomes]
rs151589	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs163444	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs164709	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs164715	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs164789	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs171211	0.96[ASN][1000 genomes]
rs171212	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs184747	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1976103	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2130757	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2171148	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2172056	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2242350	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2291519	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2291520	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2450230	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28602964	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28768211	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2930945	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2930949	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2930951	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2932772	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2932773	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2932775	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2932776	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2932782	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2972361	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2972366	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2972377	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2972378	0.84[AMR][1000 genomes]
rs2972381	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2972386	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2972387	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2972388	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34893396	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350106	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs350107	1.00[CEU][hapmap];0.94[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs350109	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs350115	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs350116	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs350122	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs350123	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs351424	0.88[YRI][hapmap]
rs35308484	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs353656	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs386640	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3890705	0.86[ASN][1000 genomes]
rs4077460	0.81[AMR][1000 genomes]
rs419902	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs426392	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4362903	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs488498	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs603029	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62373181	0.80[ASN][1000 genomes]
rs6450026	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6450027	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs676012	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs676879	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6876783	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs693725	1.00[CEU][hapmap];0.94[YRI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs350104	CCDC125	cis	lung	GTEx
rs350104	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs350104	MRPS36	cis	lymphoblastoid	seeQTL
rs350104	TAF9	cis	Esophagus Muscularis	GTEx
rs350104	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68461600-68464000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr5:68461800-68462600	Enhancers	Lung	lung
3	chr5:68461800-68462600	Enhancers	Pancreas	Pancrea
4	chr5:68461800-68462800	Flanking Active TSS	Dnd41	blood
5	chr5:68462000-68462600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
6	chr5:68462000-68462600	Flanking Active TSS	Brain Cingulate Gyrus	brain
7	chr5:68462000-68463600	Active TSS	Fetal Lung	lung
8	chr5:68462000-68463800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr5:68462000-68463800	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr5:68462200-68462600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr5:68462200-68462600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
12	chr5:68462200-68462600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr5:68462200-68462600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:68462200-68462600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:68462200-68462600	Flanking Active TSS	Brain Anterior Caudate	brain
16	chr5:68462200-68462600	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr5:68462200-68462600	Flanking Active TSS	Fetal Heart	heart
18	chr5:68462200-68462600	Flanking Active TSS	A549	lung
19	chr5:68462200-68462600	Flanking Active TSS	Hela-S3	cervix
20	chr5:68462200-68462600	Flanking Active TSS	HepG2	liver
21	chr5:68462200-68462600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr5:68462200-68462600	Flanking Active TSS	NHDF-Ad	bronchial
23	chr5:68462200-68462600	Flanking Active TSS	NHEK	skin
24	chr5:68462200-68462600	Flanking Active TSS	Osteobl	bone
25	chr5:68462200-68462800	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr5:68462200-68462800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:68462200-68462800	Enhancers	Stomach Mucosa	stomach
28	chr5:68462200-68463000	Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr5:68462200-68463200	Active TSS	Brain Angular Gyrus	brain
30	chr5:68462200-68463200	Active TSS	Brain Hippocampus Middle	brain
31	chr5:68462200-68463200	Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr5:68462200-68463200	Active TSS	Fetal Muscle Trunk	muscle
33	chr5:68462200-68463400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr5:68462200-68463400	Active TSS	Rectal Mucosa Donor 29	rectum
35	chr5:68462200-68463600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr5:68462200-68463600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr5:68462200-68463600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:68462200-68463600	Active TSS	Brain Germinal Matrix	brain
39	chr5:68462200-68463600	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr5:68462200-68463600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
41	chr5:68462200-68463600	Active TSS	Colon Smooth Muscle	Colon
42	chr5:68462200-68463600	Active TSS	K562	blood
43	chr5:68462200-68463600	Active TSS	NHLF	lung
44	chr5:68462200-68463800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr5:68462200-68463800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:68462200-68463800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr5:68462200-68463800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr5:68462200-68464200	Active TSS	Fetal Kidney	kidney
49	chr5:68462400-68462600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
50	chr5:68462400-68462600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell

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