Variant report

Variant	rs1264694
Chromosome Location	chr6:30068724-30068725
allele	G/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	CTCF	chr6:30068660-30068810	SK-N-SH_RA	brain:	n/a	n/a
2	TAF1	chr6:30068456-30068947	HepG2	liver:	n/a	n/a
3	POLR2A	chr6:30068645-30068993	Raji	blood:	n/a	n/a
4	CTCF	chr6:30068720-30068870	HEK293	kidney:	n/a	n/a
5	CTCF	chr6:30068680-30068830	SAEC	small airway:	n/a	n/a
6	FOXA1	chr6:30068083-30068783	HepG2	liver:	n/a	n/a
7	HDAC2	chr6:30068189-30069146	HepG2	liver:	n/a	n/a
8	YY1	chr6:30068238-30068998	HepG2	liver:	n/a	chr6:30068731-30068745
9	POLR2A	chr6:30068466-30068989	MCF-7	breast:	n/a	n/a
10	MAX	chr6:30068086-30071338	HCT-116	colon:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
11	NFIC	chr6:30068212-30069001	HepG2	liver:	n/a	n/a
12	MBD4	chr6:30068218-30069187	HepG2	liver:	n/a	n/a
13	POLR2A	chr6:30068340-30069000	HepG2	liver:	n/a	n/a
14	HNF4A	chr6:30068131-30068787	HepG2	liver:	n/a	chr6:30068534-30068542 chr6:30068408-30068423
15	CTCF	chr6:30068620-30068770	AG04449	skin:	n/a	n/a
16	CTCF	chr6:30068685-30068831	MCF-7	breast:	n/a	n/a
17	TEAD4	chr6:30068212-30069469	HepG2	liver:	n/a	n/a
18	CEBPD	chr6:30068391-30068962	HepG2	liver:	n/a	n/a
19	POLR2A	chr6:30068407-30068921	HCT-116	colon:	n/a	n/a
20	REST	chr6:30068255-30068900	HepG2	liver:	n/a	chr6:30068619-30068632
21	MAX	chr6:30068271-30068997	H1-hESC	embryonic stem cell:	n/a	chr6:30068716-30068725
22	POLR2A	chr6:30068376-30071409	HepG2	liver:	n/a	n/a
23	POLR2A	chr6:30068503-30068913	HepG2	liver:	n/a	n/a
24	CTCF	chr6:30068620-30068770	WERI-Rb-1	eye:	n/a	n/a
25	CTCF	chr6:30068685-30068872	MCF-7	breast:	n/a	n/a
26	HA-E2F1	chr6:30068327-30069039	MCF-7	breast:	n/a	chr6:30068406-30068413
27	HNF4A	chr6:30068230-30068865	HepG2	liver:	n/a	chr6:30068534-30068542 chr6:30068408-30068423
28	FOXA1	chr6:30068153-30068836	HepG2	liver:	n/a	n/a
29	MAX	chr6:30067884-30071564	HepG2	liver:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
30	POLR2A	chr6:30068532-30068887	MCF-7	breast:	n/a	n/a
31	MAX	chr6:30068557-30068891	HepG2	liver:	n/a	chr6:30068716-30068725
32	POLR2A	chr6:30068290-30071350	HepG2	liver:	n/a	n/a
33	MXI1	chr6:30068445-30068932	HepG2	liver:	n/a	n/a
34	GABPA	chr6:30068355-30069046	MCF-7	breast:	n/a	n/a
35	MYBL2	chr6:30068021-30071300	HepG2	liver:	n/a	n/a
36	MYC	chr6:30068574-30070009	MCF10A-Er-Src	breast:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
37	EGR1	chr6:30068594-30068867	K562	blood:	n/a	chr6:30068696-30068706 chr6:30068731-30068744
38	CTCF	chr6:30068640-30068790	GM12875	blood:	n/a	n/a
39	MAX	chr6:30068117-30069148	HCT-116	colon:	n/a	chr6:30068716-30068725
40	E2F6	chr6:30068537-30068845	K562	blood:	n/a	n/a
41	TEAD4	chr6:30068418-30068977	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr6:30068584-30068738	MCF-7	breast:	n/a	n/a
43	CTCF	chr6:30068720-30068870	HCFaa	heart:	n/a	n/a
44	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
45	TCF12	chr6:30068280-30069054	ECC-1	luminal epithelium:	n/a	chr6:30068688-30068695 chr6:30068646-30068654
46	MAX	chr6:30068260-30070212	MCF-7	breast:	n/a	chr6:30069316-30069323 chr6:30069315-30069324 chr6:30068716-30068725
47	MAX	chr6:30068195-30068992	ECC-1	luminal epithelium:	n/a	chr6:30068716-30068725
48	EGR1	chr6:30068581-30068995	ECC-1	luminal epithelium:	n/a	chr6:30068696-30068706 chr6:30068731-30068744
49	CTCF	chr6:30068680-30068830	GM12875	blood:	n/a	n/a
50	MYC	chr6:30068427-30068928	HepG2	liver:	n/a	chr6:30068716-30068725

No.	Distal block	Cell Line	Cell type
1	chr6:30043035..30044565-chr6:30066202..30069074,2	MCF-7	breast:
2	chr6:30031338..30034907-chr6:30068673..30070684,4	MCF-7	breast:
3	chr6:30039673..30045870-chr6:30065915..30071954,9	MCF-7	breast:
4	chr6:30059482..30063646-chr6:30064744..30071169,8	MCF-7	breast:
5	chr6:30037077..30039641-chr6:30068261..30070312,3	MCF-7	breast:
6	chr6:30068376..30069897-chr6:30103951..30105962,2	MCF-7	breast:
7	chr6:30068684..30075353-chr6:30179679..30184952,7	MCF-7	breast:
8	chr6:30004933..30007814-chr6:30068168..30069816,2	MCF-7	breast:
9	chr6:30029240..30031636-chr6:30067690..30069434,2	K562	blood:
10	chr6:30031856..30036259-chr6:30064937..30071315,10	MCF-7	breast:
11	chr6:30027986..30030809-chr6:30067690..30071011,4	K562	blood:
12	chr6:30059663..30061808-chr6:30067229..30070058,2	K562	blood:
13	chr6:30028086..30030535-chr6:30068315..30071049,3	MCF-7	breast:
14	chr6:30067195..30070112-chr6:30098151..30100617,2	MCF-7	breast:
15	chr6:30039276..30042217-chr6:30067253..30069841,2	K562	blood:
16	chr6:30024946..30027912-chr6:30068442..30070614,2	MCF-7	breast:
17	chr6:30068547..30070487-chr6:30073986..30076858,2	K562	blood:
18	chr6:30063791..30066840-chr6:30067476..30070156,3	MCF-7	breast:
19	chr6:30067592..30070049-chr6:30312859..30314391,2	K562	blood:
20	chr6:30046314..30047956-chr6:30068316..30070912,2	MCF-7	breast:

Variant related genes	Relation type
TRIM31-AS1	TF binding region
ENSG00000204619	Chromatin interaction
ENSG00000234127	Chromatin interaction
ENSG00000241370	Chromatin interaction
ENSG00000204614	Chromatin interaction
ENSG00000204616	Chromatin interaction
ENSG00000066379	Chromatin interaction
ENSG00000204618	Chromatin interaction
ENSG00000204623	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1108052	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1108053	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1110446	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1110448	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1156533	0.84[ASN][1000 genomes]
rs11751554	0.83[ASN][1000 genomes]
rs11967911	0.90[ASN][1000 genomes]
rs11968367	0.83[ASN][1000 genomes]
rs11968434	0.83[ASN][1000 genomes]
rs1264695	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1264696	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1264702	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12661731	0.84[ASN][1000 genomes]
rs17187791	0.90[ASN][1000 genomes]
rs17187805	0.90[ASN][1000 genomes]
rs17194146	0.82[ASN][1000 genomes]
rs17194153	0.90[ASN][1000 genomes]
rs17194160	0.90[ASN][1000 genomes]
rs17194174	0.90[ASN][1000 genomes]
rs2072110	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2240071	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2248289	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2523994	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2844796	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28454792	0.89[ASN][1000 genomes]
rs28780078	0.84[ASN][1000 genomes]
rs28780079	0.84[ASN][1000 genomes]
rs28780080	0.84[ASN][1000 genomes]
rs28780081	0.90[ASN][1000 genomes]
rs28780082	0.83[ASN][1000 genomes]
rs57195817	0.81[ASN][1000 genomes]
rs60418878	0.82[ASN][1000 genomes]
rs61666432	0.83[ASN][1000 genomes]
rs6457149	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73424274	0.82[ASN][1000 genomes]
rs7741418	0.84[ASN][1000 genomes]
rs7749793	0.90[ASN][1000 genomes]
rs7753935	0.90[ASN][1000 genomes]
rs7754005	0.90[ASN][1000 genomes]
rs7761563	0.84[ASN][1000 genomes]
rs7765810	0.84[ASN][1000 genomes]
rs7771071	0.83[ASN][1000 genomes]
rs916569	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs916570	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9261384	0.84[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1264694	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs1264694	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1264694	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30064800-30069600	Bivalent Enhancer	Fetal Thymus	thymus
2	chr6:30065400-30068800	Weak transcription	Gastric	stomach
3	chr6:30067800-30069000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
4	chr6:30068000-30068800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
5	chr6:30068000-30068800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
6	chr6:30068000-30068800	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:30068000-30068800	Bivalent Enhancer	Fetal Lung	lung
8	chr6:30068000-30068800	Enhancers	K562	blood
9	chr6:30068000-30068800	Bivalent Enhancer	NHDF-Ad	bronchial
10	chr6:30068000-30069000	Bivalent Enhancer	Liver	Liver
11	chr6:30068000-30069200	Bivalent Enhancer	Placenta	Placenta
12	chr6:30068000-30069800	Enhancers	Lung	lung
13	chr6:30068000-30072600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
14	chr6:30068200-30068800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
15	chr6:30068200-30068800	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:30068200-30068800	Active TSS	Breast Myoepithelial Primary Cells	Breast
17	chr6:30068200-30068800	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
18	chr6:30068200-30068800	Enhancers	Stomach Mucosa	stomach
19	chr6:30068200-30069000	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr6:30068200-30069000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
21	chr6:30068200-30069000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:30068200-30069200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr6:30068200-30069400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
24	chr6:30068200-30069800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:30068200-30069800	Flanking Active TSS	Duodenum Mucosa	Duodenum
26	chr6:30068200-30070200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:30068200-30071800	Flanking Active TSS	NHEK	skin
28	chr6:30068400-30068800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr6:30068400-30068800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
30	chr6:30068400-30068800	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
31	chr6:30068400-30068800	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr6:30068400-30068800	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:30068400-30068800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr6:30068400-30068800	Bivalent Enhancer	Brain Angular Gyrus	brain
35	chr6:30068400-30068800	Bivalent Enhancer	Brain Substantia Nigra	brain
36	chr6:30068400-30068800	Bivalent Enhancer	Fetal Brain Female	brain
37	chr6:30068400-30068800	Bivalent/Poised TSS	Fetal Intestine Large	intestine
38	chr6:30068400-30068800	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr6:30068400-30068800	Flanking Active TSS	Right Atrium	heart
40	chr6:30068400-30068800	Bivalent/Poised TSS	HepG2	liver
41	chr6:30068400-30068800	Bivalent Enhancer	HUVEC	blood vessel
42	chr6:30068400-30069000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr6:30068400-30069000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
44	chr6:30068400-30069000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr6:30068400-30069000	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
46	chr6:30068400-30069000	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr6:30068400-30069000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:30068400-30069000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr6:30068400-30069000	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr6:30068400-30069000	Flanking Bivalent TSS/Enh	Psoas Muscle	Psoas

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