Variant report

Variant	rs9401094
Chromosome Location	chr6:119217675-119217676
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	KAP1	chr6:119217431-119217999	HEK293	kidney:	n/a	chr6:119217602-119217611
2	EP300	chr6:119217515-119218021	A549	lung:	n/a	chr6:119217827-119217836
3	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
4	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
5	YY1	chr6:119217404-119217986	SK-N-SH_RA	brain:	n/a	n/a
6	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
7	POLR2A	chr6:119217373-119217948	U87	brain:	n/a	n/a
8	EBF1	chr6:119217509-119217914	GM12878	blood:	n/a	n/a
9	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
10	EP300	chr6:119217417-119218046	K562	blood:	n/a	chr6:119217827-119217836
11	NFIC	chr6:119217237-119218081	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:119217396-119217827	HepG2	liver:	n/a	n/a
13	CTCF	chr6:119217405-119218070	K562	blood:	n/a	n/a
14	MAFF	chr6:119217427-119218045	K562	blood:	n/a	chr6:119217819-119217837
15	CEBPB	chr6:119217426-119218188	A549	lung:	n/a	n/a
16	TCF12	chr6:119217450-119218105	A549	lung:	n/a	n/a
17	CTCF	chr6:119217620-119217770	GM12875	blood:	n/a	n/a
18	EP300	chr6:119217443-119218018	A549	lung:	n/a	chr6:119217827-119217836
19	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
20	EP300	chr6:119217427-119217983	Hela-S3	cervix:	n/a	chr6:119217827-119217836
21	TRIM28	chr6:119217378-119218157	K562	blood:	n/a	chr6:119217602-119217611
22	MAFK	chr6:119217442-119218017	HepG2	liver:	n/a	chr6:119217604-119217614 chr6:119217821-119217836
23	IRF1	chr6:119217420-119218010	K562	blood:	n/a	chr6:119217828-119217837 chr6:119217768-119217778 chr6:119217770-119217779
24	POLR2A	chr6:119217485-119217779	H1-neurons	neurons:	n/a	n/a
25	CTCF	chr6:119217540-119217690	HA-sp	spinal cord:	n/a	n/a
26	FOXM1	chr6:119217374-119218041	GM12878	blood:	n/a	n/a
27	IRF1	chr6:119217281-119217930	K562	blood:	n/a	chr6:119217828-119217837 chr6:119217768-119217778 chr6:119217770-119217779
28	BCLAF1	chr6:119217433-119217948	GM12878	blood:	n/a	chr6:119217769-119217778
29	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
30	CTCF	chr6:119217385-119218112	A549	lung:	n/a	n/a
31	CBX3	chr6:119217451-119218031	K562	blood:	n/a	chr6:119217965-119217976
32	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
33	PML	chr6:119217331-119218033	K562	blood:	n/a	chr6:119217602-119217611
34	YY1	chr6:119217366-119217968	GM12892	blood:	n/a	n/a
35	YY1	chr6:119217451-119217949	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr6:119217232-119218035	U87	brain:	n/a	n/a
37	TBP	chr6:119217505-119217776	HepG2	liver:	n/a	n/a
38	MXI1	chr6:119217518-119217933	HepG2	liver:	n/a	n/a
39	MYC	chr6:119217456-119218035	MCF10A-Er-Src	breast:	n/a	chr6:119217604-119217613 chr6:119217827-119217836
40	MYC	chr6:119217451-119218024	K562	blood:	n/a	chr6:119217604-119217613 chr6:119217827-119217836
41	TBP	chr6:119217518-119217786	K562	blood:	n/a	n/a
42	CBX3	chr6:119217383-119218151	HCT-116	colon:	n/a	chr6:119217965-119217976
43	CBX3	chr6:119217409-119218274	K562	blood:	n/a	chr6:119217965-119217976
44	FOS	chr6:119217450-119218033	HUVEC	blood vessel:	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
45	CEBPB	chr6:119217434-119217795	IMR90	lung:	n/a	n/a
46	POLR2A	chr6:119217360-119217763	U87	brain:	n/a	n/a
47	CEBPB	chr6:119217334-119217948	K562	blood:	n/a	n/a
48	BATF	chr6:119217572-119217931	GM12878	blood:	n/a	chr6:119217601-119217611
49	YY1	chr6:119217471-119217695	HCT-116	colon:	n/a	n/a
50	POLR2A	chr6:119217320-119218549	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:119217672-119217722	AG04450	lung:	fetal
2	chr6:119217672-119217722	HepG2	liver:	n/a
3	chr6:119217672-119217722	ECC-1	luminal epithelium:	n/a
4	chr6:119217672-119217722	HCT-116	colon:	n/a
5	chr6:119217672-119217722	HUVEC	blood vessel:	n/a
6	chr6:119217672-119217722	HCM	heart:	n/a
7	chr6:119217672-119217722	SK-N-MC	brain:	n/a
8	chr6:119217672-119217722	AG09309	skin:	n/a
9	chr6:119217672-119217722	HCF	heart:	n/a
10	chr6:119217672-119217722	Hela-S3	cervix:	n/a
11	chr6:119217672-119217722	SAEC	small airway:	n/a
12	chr6:119217672-119217722	HPAEpiC	pulmonary alveolar:	n/a
13	chr6:119217672-119217722	HEK293	kidney:	embryo
14	chr6:119217672-119217722	AG10803	skin:	n/a
15	chr6:119217672-119217722	ProgFib	skin:	n/a
16	chr6:119217672-119217722	CMK	blood:	n/a
17	chr6:119217672-119217722	RPTEC	kidney:	n/a
18	chr6:119217672-119217722	PrEC	prostate:	n/a
19	chr6:119217672-119217722	HEEpiC	esophagus:	n/a
20	chr6:119217672-119217722	U87	brain:	n/a
21	chr6:119217672-119217722	GM06990	blood:	n/a
22	chr6:119217672-119217722	AG09319	gingival:	n/a
23	chr6:119217672-119217722	Hepatocyte	liver:	n/a
24	chr6:119217672-119217722	HCPEpiC	choroid plexus:	n/a
25	chr6:119217672-119217722	NHDF-neo	bronchial:	n/a
26	chr6:119217672-119217722	NT2-D1	testis:	n/a
27	chr6:119217672-119217722	MCF-7	breast:	n/a
28	chr6:119217672-119217722	HAEpiC	amniotic membrane:	n/a
29	chr6:119217672-119217722	K562	blood:	n/a
30	chr6:119217672-119217722	HNPCEpiC	eye:	n/a
31	chr6:119217672-119217722	SK-N-SH	brain:	n/a
32	chr6:119217672-119217722	HRPEpiC	eye:	n/a
33	chr6:119217672-119217722	HIPEpiC	eye:	n/a
34	chr6:119217672-119217722	NHBE	bronchial:	n/a
35	chr6:119217672-119217722	AG04449	skin:	fetal
36	chr6:119217672-119217722	GM12878	blood:	n/a
37	chr6:119217672-119217722	HRE	kidney:	n/a
38	chr6:119217672-119217722	HMEC	breast:	n/a
39	chr6:119217672-119217722	T-47D	breast:	n/a
40	chr6:119217672-119217722	HRCEpiC	kidney:	n/a
41	chr6:119217672-119217722	SKMC	muscle:	n/a
42	chr6:119217672-119217722	PANC-1	pancreas:	n/a
43	chr6:119217672-119217722	ovcar-3	ovarian:	n/a
44	chr6:119217672-119217722	AoSMC	blood vessel:	n/a
45	chr6:119217672-119217722	A549	lung:	n/a
46	chr6:119217672-119217722	NH-A	brain:	n/a
47	chr6:119217672-119217722	H1-hESC	embryonic stem cell:	embryo
48	chr6:119217672-119217722	LNCaP	prostate:	n/a
49	chr6:119217672-119217722	BJ	skin:	n/a
50	chr6:119217672-119217722	PFSK-1	brain:	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	chr5:140698166..140700662-chr6:119215254..119217886,2	MCF-7	breast:
8	chr6:119215924..119218586-chr6:119236069..119238504,2	K562	blood:
9	chr6:118997357..119000224-chr6:119215620..119217691,2	K562	blood:
10	chr6:119027193..119028788-chr6:119215908..119217917,2	K562	blood:
11	chr6:119029203..119032181-chr6:119214720..119218048,3	K562	blood:
12	chr6:119216161..119219506-chr6:119398191..119401599,4	K562	blood:

Variant related genes	Relation type
MCM9	TF binding region
MCM9	CpG island
ENSG00000178913	Chromatin interaction
ENSG00000253194	Chromatin interaction
ENSG00000111879	Chromatin interaction
ENSG00000255729	Chromatin interaction
ENSG00000111877	Chromatin interaction
ENSG00000111860	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11153781	0.91[ASN][1000 genomes]
rs11153791	0.95[ASN][1000 genomes]
rs12207663	0.95[ASN][1000 genomes]
rs12213327	0.95[ASN][1000 genomes]
rs1775613	1.00[JPT][hapmap]
rs3756939	1.00[JPT][hapmap]
rs4343954	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61299241	1.00[AMR][1000 genomes]
rs67182660	1.00[ASN][1000 genomes]
rs6902942	0.95[ASN][1000 genomes]
rs7775275	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs794249	1.00[JPT][hapmap]
rs9372515	0.85[AMR][1000 genomes]
rs9372521	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9374756	1.00[ASN][1000 genomes]
rs9374760	0.95[ASN][1000 genomes]
rs9374762	0.95[ASN][1000 genomes]
rs9374769	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9374770	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9385059	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9385066	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9387602	0.85[AMR][1000 genomes]
rs9387607	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9387618	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9387623	1.00[AMR][1000 genomes]
rs9387627	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9401092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9401095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9401096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9401100	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9401101	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9401110	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9401111	1.00[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs9401112	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9401117	1.00[AFR][1000 genomes];1.00[AMR][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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:119213400-119217800	Active TSS	Right Atrium	heart
2	chr6:119213600-119217800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr6:119213600-119218000	Active TSS	Primary T cells fromperipheralblood	blood
4	chr6:119213600-119218200	Active TSS	NHLF	lung
5	chr6:119213800-119218000	Active TSS	GM12878-XiMat	blood
6	chr6:119213800-119218200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
7	chr6:119214000-119217800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:119214000-119218000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:119214000-119218000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:119214200-119217800	Active TSS	Rectal Mucosa Donor 29	rectum
11	chr6:119214200-119218200	Active TSS	H9 Cell Line	embryonic stem cell
12	chr6:119214400-119218000	Active TSS	HMEC	breast
13	chr6:119214400-119218200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr6:119214600-119217800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:119214600-119218000	Active TSS	K562	blood
16	chr6:119214600-119218200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:119216200-119217800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr6:119216200-119218000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr6:119216400-119217800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr6:119216400-119218000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:119216600-119217800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr6:119216600-119217800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr6:119216600-119218000	Weak transcription	Left Ventricle	heart
24	chr6:119216600-119218000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr6:119216600-119219600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr6:119216600-119220200	Weak transcription	Pancreas	Pancrea
27	chr6:119216600-119220200	Weak transcription	Spleen	Spleen
28	chr6:119216600-119220400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:119216600-119220400	Weak transcription	Esophagus	oesophagus
30	chr6:119216600-119224400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:119216600-119233800	Weak transcription	Lung	lung
32	chr6:119216600-119236600	Weak transcription	Gastric	stomach
33	chr6:119216600-119243800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr6:119216800-119217800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr6:119216800-119217800	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr6:119216800-119217800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
37	chr6:119216800-119217800	Enhancers	Adipose Nuclei	Adipose
38	chr6:119216800-119217800	Enhancers	Duodenum Smooth Muscle	Duodenum
39	chr6:119216800-119217800	Weak transcription	Psoas Muscle	Psoas
40	chr6:119216800-119218000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr6:119216800-119218200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr6:119216800-119218200	Weak transcription	Fetal Intestine Small	intestine
43	chr6:119216800-119218600	Enhancers	Primary B cells from peripheral blood	blood
44	chr6:119216800-119219200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr6:119216800-119219200	Weak transcription	Placenta	Placenta
46	chr6:119216800-119219600	Weak transcription	HSMM	muscle
47	chr6:119216800-119220200	Weak transcription	Right Ventricle	heart
48	chr6:119216800-119230600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:119216800-119232400	Weak transcription	Colonic Mucosa	Colon
50	chr6:119216800-119232600	Weak transcription	Placenta Amnion	Placenta Amnion

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