Variant report

Variant	rs4946367
Chromosome Location	chr6:119217940-119217941
allele	A/G
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	KAP1	chr6:119217431-119217999	HEK293	kidney:	n/a	chr6:119217602-119217611
2	EP300	chr6:119217515-119218021	A549	lung:	n/a	chr6:119217827-119217836
3	CTCF	chr6:119217840-119217990	NHEK	skin:	n/a	n/a
4	JUND	chr6:119217495-119217992	SK-N-SH	brain:	n/a	chr6:119217828-119217836 chr6:119217829-119217836 chr6:119217604-119217611 chr6:119217826-119217837 chr6:119217604-119217612 chr6:119217828-119217836 chr6:119217603-119217613 chr6:119217604-119217612
5	FOSL1	chr6:119217236-119218166	HCT-116	colon:	n/a	chr6:119217828-119217836 chr6:119217829-119217836 chr6:119217604-119217611 chr6:119217604-119217612 chr6:119217828-119217836 chr6:119217603-119217613 chr6:119217604-119217612
6	YY1	chr6:119217404-119217986	SK-N-SH_RA	brain:	n/a	n/a
7	FOS	chr6:119217388-119218023	MCF10A-Er-Src	breast:	n/a	chr6:119217828-119217836 chr6:119217826-119217837 chr6:119217829-119217836 chr6:119217604-119217611 chr6:119217604-119217612 chr6:119217828-119217836 chr6:119217603-119217613 chr6:119217604-119217612
8	CTCF	chr6:119217820-119217970	GM12872	blood:	n/a	n/a
9	POLR2A	chr6:119217373-119217948	U87	brain:	n/a	n/a
10	CTCF	chr6:119217800-119217950	GM12866	blood:	n/a	n/a
11	CTCF	chr6:119217694-119218009	K562	blood:	n/a	n/a
12	JUND	chr6:119217406-119218138	HCT-116	colon:	n/a	chr6:119217828-119217836 chr6:119217829-119217836 chr6:119217604-119217611 chr6:119217826-119217837 chr6:119217604-119217612 chr6:119217828-119217836 chr6:119217603-119217613 chr6:119217604-119217612
13	EP300	chr6:119217417-119218046	K562	blood:	n/a	chr6:119217827-119217836
14	RAD21	chr6:119217685-119217974	GM12878	blood:	n/a	n/a
15	NFIC	chr6:119217237-119218081	GM12878	blood:	n/a	n/a
16	CTCF	chr6:119217800-119217950	HEK293	kidney:	n/a	n/a
17	CTCF	chr6:119217773-119217995	MCF-7	breast:	n/a	n/a
18	CTCF	chr6:119217405-119218070	K562	blood:	n/a	n/a
19	CTCF	chr6:119217820-119217970	SK-N-SH_RA	brain:	n/a	n/a
20	CTCF	chr6:119217820-119217970	AG10803	skin:	n/a	n/a
21	MAFF	chr6:119217427-119218045	K562	blood:	n/a	chr6:119217819-119217837
22	CEBPB	chr6:119217426-119218188	A549	lung:	n/a	n/a
23	CTCF	chr6:119217820-119217970	HUVEC	blood vessel:	n/a	n/a
24	TCF12	chr6:119217450-119218105	A549	lung:	n/a	n/a
25	EP300	chr6:119217443-119218018	A549	lung:	n/a	chr6:119217827-119217836
26	CTCF	chr6:119217840-119217990	K562	blood:	n/a	n/a
27	CTCF	chr6:119217820-119217970	HBMEC	blood vessel:	n/a	n/a
28	JUND	chr6:119217411-119218006	HepG2	liver:	n/a	chr6:119217828-119217836 chr6:119217829-119217836 chr6:119217604-119217611 chr6:119217826-119217837 chr6:119217604-119217612 chr6:119217828-119217836 chr6:119217603-119217613 chr6:119217604-119217612
29	CTCF	chr6:119217800-119217950	WI-38	lung:	n/a	n/a
30	EP300	chr6:119217427-119217983	Hela-S3	cervix:	n/a	chr6:119217827-119217836
31	CTCF	chr6:119217829-119217950	GM10248	blood:	n/a	n/a
32	USF2	chr6:119217888-119218080	Hela-S3	cervix:	n/a	n/a
33	TRIM28	chr6:119217378-119218157	K562	blood:	n/a	chr6:119217602-119217611
34	CTCF	chr6:119217820-119217970	HepG2	liver:	n/a	n/a
35	MAFK	chr6:119217442-119218017	HepG2	liver:	n/a	chr6:119217604-119217614 chr6:119217821-119217836
36	IRF1	chr6:119217420-119218010	K562	blood:	n/a	chr6:119217828-119217837 chr6:119217768-119217778 chr6:119217770-119217779
37	CTCF	chr6:119217840-119217990	AG09319	gingival:	n/a	n/a
38	FOXM1	chr6:119217374-119218041	GM12878	blood:	n/a	n/a
39	BCLAF1	chr6:119217433-119217948	GM12878	blood:	n/a	chr6:119217769-119217778
40	JUND	chr6:119217499-119218032	H1-hESC	embryonic stem cell:	n/a	chr6:119217828-119217836 chr6:119217829-119217836 chr6:119217604-119217611 chr6:119217826-119217837 chr6:119217604-119217612 chr6:119217828-119217836 chr6:119217603-119217613 chr6:119217604-119217612
41	CTCF	chr6:119217820-119217970	SAEC	small airway:	n/a	n/a
42	CTCF	chr6:119217385-119218112	A549	lung:	n/a	n/a
43	CTCF	chr6:119217820-119217970	NHLF	lung:	n/a	n/a
44	CTCF	chr6:119217820-119217970	Caco-2	colon:	n/a	n/a
45	CBX3	chr6:119217451-119218031	K562	blood:	n/a	chr6:119217965-119217976
46	FOS	chr6:119217336-119217996	MCF10A-Er-Src	breast:	n/a	chr6:119217828-119217836 chr6:119217826-119217837 chr6:119217829-119217836 chr6:119217604-119217611 chr6:119217604-119217612 chr6:119217828-119217836 chr6:119217603-119217613 chr6:119217604-119217612
47	CTCF	chr6:119217817-119217954	Hela-S3	cervix:	n/a	n/a
48	CTCF	chr6:119217788-119217952	HepG2	liver:	n/a	n/a
49	PML	chr6:119217331-119218033	K562	blood:	n/a	chr6:119217602-119217611
50	CTCF	chr6:119217800-119217950	AG04450	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:119214552..119219906-chr6:119253918..119257622,8	MCF-7	breast:
2	chr6:119216722..119218492-chr6:119251658..119253168,2	K562	blood:
3	chr6:119213105..119220728-chr6:119253299..119257962,22	K562	blood:
4	chr6:119213694..119219544-chr6:119251621..119258172,21	K562	blood:
5	chr6:119030681..119033583-chr6:119216548..119219009,2	K562	blood:
6	chr6:119215906..119219234-chr6:119443291..119446175,3	K562	blood:
7	chr6:119217885..119221356-chr6:119243903..119247955,3	K562	blood:
8	chr6:119215924..119218586-chr6:119236069..119238504,2	K562	blood:
9	chr6:119029203..119032181-chr6:119214720..119218048,3	K562	blood:
10	chr6:119217885..119219986-chr6:119244920..119246613,2	K562	blood:
11	chr6:119216161..119219506-chr6:119398191..119401599,4	K562	blood:

Variant related genes	Relation type
MCM9	TF binding region
ENSG00000253194	Chromatin interaction
ENSG00000111877	Chromatin interaction
ENSG00000111860	Chromatin interaction
ENSG00000111879	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs1022706	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1022707	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1022708	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1022709	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11153782	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11965951	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11967231	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11967232	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1807979	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1885125	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2145569	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2145570	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2180860	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35906538	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3945959	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4245502	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946369	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946370	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946371	0.82[ASN][1000 genomes]
rs4946372	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946373	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946374	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946376	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946377	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946378	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4946380	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4946381	0.85[EUR][1000 genomes]
rs55978448	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56022752	0.85[EUR][1000 genomes]
rs62422265	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62422266	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62422267	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62422268	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62422269	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62422270	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6569035	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6901738	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6903220	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6903579	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6904381	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6910377	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6916291	0.83[EUR][1000 genomes]
rs6916491	0.85[ASN][1000 genomes]
rs6916672	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6918569	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6918844	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6919100	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6923637	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6923771	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6928315	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6928945	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6931423	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6932585	0.81[ASN][1000 genomes]
rs6933970	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6935960	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6939937	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6940120	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7381533	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7381535	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7381546	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7741149	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7758729	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7758849	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7758862	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7759423	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9320669	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9320670	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9320671	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9374759	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9374763	0.91[EUR][1000 genomes]
rs9374764	0.89[EUR][1000 genomes]
rs9374765	0.89[EUR][1000 genomes]
rs9374766	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9374767	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9385060	0.91[EUR][1000 genomes]
rs9385063	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9387610	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9387611	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9387612	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9387613	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9401099	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9401103	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9401106	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9489563	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9489569	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9689589	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs988098	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9968863	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020405	chr6:118786586-119241006	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1023826	chr6:119026481-119221408	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4946367	MCM9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119213600-119218000	Active TSS	Primary T cells fromperipheralblood	blood
2	chr6:119213600-119218200	Active TSS	NHLF	lung
3	chr6:119213800-119218000	Active TSS	GM12878-XiMat	blood
4	chr6:119213800-119218200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
5	chr6:119214000-119218000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr6:119214000-119218000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:119214200-119218200	Active TSS	H9 Cell Line	embryonic stem cell
8	chr6:119214400-119218000	Active TSS	HMEC	breast
9	chr6:119214400-119218200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr6:119214600-119218000	Active TSS	K562	blood
11	chr6:119214600-119218200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr6:119216200-119218000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr6:119216400-119218000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:119216600-119218000	Weak transcription	Left Ventricle	heart
15	chr6:119216600-119218000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr6:119216600-119219600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:119216600-119220200	Weak transcription	Pancreas	Pancrea
18	chr6:119216600-119220200	Weak transcription	Spleen	Spleen
19	chr6:119216600-119220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr6:119216600-119220400	Weak transcription	Esophagus	oesophagus
21	chr6:119216600-119224400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr6:119216600-119233800	Weak transcription	Lung	lung
23	chr6:119216600-119236600	Weak transcription	Gastric	stomach
24	chr6:119216600-119243800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:119216800-119218000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:119216800-119218200	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr6:119216800-119218200	Weak transcription	Fetal Intestine Small	intestine
28	chr6:119216800-119218600	Enhancers	Primary B cells from peripheral blood	blood
29	chr6:119216800-119219200	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr6:119216800-119219200	Weak transcription	Placenta	Placenta
31	chr6:119216800-119219600	Weak transcription	HSMM	muscle
32	chr6:119216800-119220200	Weak transcription	Right Ventricle	heart
33	chr6:119216800-119230600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr6:119216800-119232400	Weak transcription	Colonic Mucosa	Colon
35	chr6:119216800-119232600	Weak transcription	Placenta Amnion	Placenta Amnion
36	chr6:119216800-119233200	Weak transcription	Aorta	Aorta
37	chr6:119216800-119235800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr6:119217000-119218000	Weak transcription	Fetal Muscle Leg	muscle
39	chr6:119217000-119218000	Active TSS	HepG2	liver
40	chr6:119217000-119218400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
41	chr6:119217000-119218400	Enhancers	Liver	Liver
42	chr6:119217000-119218600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr6:119217000-119220200	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:119217000-119223200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr6:119217000-119225400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr6:119217000-119242200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr6:119217200-119218000	Flanking Active TSS	HUVEC	blood vessel
48	chr6:119217200-119218400	Enhancers	Primary B cells from cord blood	blood
49	chr6:119217200-119219400	Enhancers	Colon Smooth Muscle	Colon
50	chr6:119217400-119218200	Enhancers	Brain Anterior Caudate	brain

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