Variant report

Variant	rs9261401
Chromosome Location	chr6:30068149-30068150
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	FOXA1	chr6:30068083-30068783	HepG2	liver:	n/a	n/a
2	MAX	chr6:30068086-30071338	HCT-116	colon:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
3	HNF4A	chr6:30068131-30068787	HepG2	liver:	n/a	chr6:30068534-30068542 chr6:30068408-30068423
4	MAX	chr6:30067884-30071564	HepG2	liver:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
5	MYBL2	chr6:30068021-30071300	HepG2	liver:	n/a	n/a
6	MAX	chr6:30068117-30069148	HCT-116	colon:	n/a	chr6:30068716-30068725
7	E2F6	chr6:30067832-30070137	H1-hESC	embryonic stem cell:	n/a	chr6:30069962-30069972 chr6:30068213-30068220 chr6:30069998-30070008 chr6:30068208-30068218 chr6:30068209-30068220 chr6:30068213-30068220 chr6:30069967-30069976 chr6:30068213-30068220 chr6:30068406-30068413 chr6:30068209-30068217 chr6:30068208-30068219 chr6:30068209-30068217
8	FOXA1	chr6:30068079-30068992	HepG2	liver:	n/a	n/a
9	SP1	chr6:30068107-30068928	HepG2	liver:	n/a	chr6:30068755-30068765 chr6:30068694-30068706
10	MYBL2	chr6:30068089-30069068	HepG2	liver:	n/a	n/a
11	NFIC	chr6:30068023-30069039	HepG2	liver:	n/a	n/a
12	MAX	chr6:30067993-30070449	HepG2	liver:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
13	MAZ	chr6:30068149-30068838	HepG2	liver:	n/a	chr6:30068716-30068725
14	EP300	chr6:30068022-30068863	HepG2	liver:	n/a	chr6:30068581-30068590 chr6:30068671-30068684
15	FOXA1	chr6:30068110-30068826	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:30043035..30044565-chr6:30066202..30069074,2	MCF-7	breast:
2	chr6:30039673..30045870-chr6:30065915..30071954,9	MCF-7	breast:
3	chr6:30059482..30063646-chr6:30064744..30071169,8	MCF-7	breast:
4	chr6:30029240..30031636-chr6:30067690..30069434,2	K562	blood:
5	chr6:30031856..30036259-chr6:30064937..30071315,10	MCF-7	breast:
6	chr6:30027986..30030809-chr6:30067690..30071011,4	K562	blood:
7	chr6:30059663..30061808-chr6:30067229..30070058,2	K562	blood:
8	chr6:30067195..30070112-chr6:30098151..30100617,2	MCF-7	breast:
9	chr6:30039276..30042217-chr6:30067253..30069841,2	K562	blood:
10	chr6:30063791..30066840-chr6:30067476..30070156,3	MCF-7	breast:
11	chr6:30067592..30070049-chr6:30312859..30314391,2	K562	blood:

Variant related genes	Relation type
TRIM31-AS1	TF binding region
ENSG00000204619	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000204618	Chromatin interaction
ENSG00000066379	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2240070	0.80[EUR][1000 genomes]
rs3094136	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6457150	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv884051	chr6:30059451-30071279	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv884050	chr6:30059451-30071330	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv884053	chr6:30059592-30070538	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
5	nsv884054	chr6:30061361-30069525	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9261401	TRIM26	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30063400-30068400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:30063600-30068200	Weak transcription	HMEC	breast
3	chr6:30064800-30068400	Bivalent Enhancer	Fetal Intestine Large	intestine
4	chr6:30064800-30069600	Bivalent Enhancer	Fetal Thymus	thymus
5	chr6:30065400-30068800	Weak transcription	Gastric	stomach
6	chr6:30066200-30068200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr6:30067000-30068200	Bivalent Enhancer	Fetal Intestine Small	intestine
8	chr6:30067000-30068400	Bivalent Enhancer	Primary T cells from cord blood	blood
9	chr6:30067600-30068200	Enhancers	Duodenum Mucosa	Duodenum
10	chr6:30067600-30068400	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
11	chr6:30067600-30068400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
12	chr6:30067800-30068200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
13	chr6:30067800-30068200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr6:30067800-30068200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:30067800-30068200	Weak transcription	Pancreas	Pancrea
16	chr6:30067800-30068200	Bivalent Enhancer	Stomach Mucosa	stomach
17	chr6:30067800-30068400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
18	chr6:30067800-30068400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
19	chr6:30067800-30068400	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr6:30067800-30068400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr6:30067800-30069000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
22	chr6:30068000-30068200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
23	chr6:30068000-30068200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
24	chr6:30068000-30068200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
25	chr6:30068000-30068200	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
26	chr6:30068000-30068200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr6:30068000-30068200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr6:30068000-30068200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
29	chr6:30068000-30068200	Flanking Bivalent TSS/Enh	Rectal Smooth Muscle	rectum
30	chr6:30068000-30068200	Flanking Active TSS	Right Ventricle	heart
31	chr6:30068000-30068200	Flanking Active TSS	HepG2	liver
32	chr6:30068000-30068400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
33	chr6:30068000-30068400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
34	chr6:30068000-30068400	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr6:30068000-30068400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
36	chr6:30068000-30068400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr6:30068000-30068400	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:30068000-30068400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
39	chr6:30068000-30068400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
40	chr6:30068000-30068400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
41	chr6:30068000-30068400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
42	chr6:30068000-30068400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr6:30068000-30068400	Active TSS	Colonic Mucosa	Colon
44	chr6:30068000-30068400	Bivalent Enhancer	Colon Smooth Muscle	Colon
45	chr6:30068000-30068400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
46	chr6:30068000-30068400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
47	chr6:30068000-30068400	Bivalent Enhancer	Psoas Muscle	Psoas
48	chr6:30068000-30068400	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
49	chr6:30068000-30068600	Bivalent/Poised TSS	Aorta	Aorta
50	chr6:30068000-30068600	Bivalent Enhancer	Brain Anterior Caudate	brain

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