Variant report

Variant	rs6759066
Chromosome Location	chr2:47082045-47082046
allele	A/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	MAX	chr2:47081762-47083224	A549	lung:	n/a	chr2:47082487-47082496 chr2:47082537-47082546 chr2:47082693-47082703 chr2:47082538-47082547
2	TCF12	chr2:47081981-47083390	SK-N-SH	brain:	n/a	chr2:47082192-47082202 chr2:47082699-47082709
3	TEAD4	chr2:47082003-47083231	SK-N-SH	brain:	n/a	n/a
4	CEBPB	chr2:47081946-47083023	A549	lung:	n/a	n/a
5	SP1	chr2:47081974-47083640	HCT-116	colon:	n/a	chr2:47082701-47082715 chr2:47082694-47082708 chr2:47083613-47083622
6	RXRA	chr2:47082019-47083030	SK-N-SH	brain:	n/a	chr2:47082538-47082547 chr2:47082537-47082546
7	EP300	chr2:47082041-47083454	SK-N-SH	brain:	n/a	chr2:47082487-47082496 chr2:47082537-47082546 chr2:47082262-47082276 chr2:47082538-47082547
8	TEAD4	chr2:47082039-47083140	SK-N-SH	brain:	n/a	n/a
9	NFIC	chr2:47081953-47083232	SK-N-SH	brain:	n/a	n/a
10	MAX	chr2:47081386-47084203	A549	lung:	n/a	chr2:47083633-47083643 chr2:47083889-47083899 chr2:47082487-47082496 chr2:47082537-47082546 chr2:47082693-47082703 chr2:47082538-47082547
11	EP300	chr2:47082035-47083215	A549	lung:	n/a	chr2:47082487-47082496 chr2:47082537-47082546 chr2:47082262-47082276 chr2:47082538-47082547
12	FOSL2	chr2:47081694-47083477	A549	lung:	n/a	chr2:47082538-47082546 chr2:47082538-47082545 chr2:47082537-47082547 chr2:47082536-47082548 chr2:47082487-47082495 chr2:47082486-47082496 chr2:47082537-47082546 chr2:47082487-47082495 chr2:47082485-47082497 chr2:47082487-47082494
13	SIX5	chr2:47081949-47083075	A549	lung:	n/a	n/a
14	FOSL1	chr2:47081768-47083460	HCT-116	colon:	n/a	chr2:47082538-47082546 chr2:47082538-47082545 chr2:47082537-47082547 chr2:47082536-47082548 chr2:47082487-47082495 chr2:47082486-47082496 chr2:47082537-47082546 chr2:47082487-47082495 chr2:47082485-47082497 chr2:47082487-47082494
15	JUND	chr2:47081997-47083410	HCT-116	colon:	n/a	chr2:47082538-47082546 chr2:47082538-47082545 chr2:47082537-47082547 chr2:47082536-47082548 chr2:47082487-47082495 chr2:47082486-47082496 chr2:47082537-47082546 chr2:47082487-47082495 chr2:47082485-47082497 chr2:47082536-47082547 chr2:47082487-47082494
16	EP300	chr2:47081815-47083256	A549	lung:	n/a	chr2:47082487-47082496 chr2:47082537-47082546 chr2:47082262-47082276 chr2:47082538-47082547
17	GATA3	chr2:47082041-47083163	SK-N-SH	brain:	n/a	chr2:47082669-47082679
18	TCF12	chr2:47081920-47083529	SK-N-SH	brain:	n/a	chr2:47082192-47082202 chr2:47082699-47082709
19	PBX3	chr2:47082025-47083220	SK-N-SH	brain:	n/a	chr2:47082316-47082327
20	FOSL1	chr2:47081943-47083223	HCT-116	colon:	n/a	chr2:47082538-47082546 chr2:47082538-47082545 chr2:47082537-47082547 chr2:47082536-47082548 chr2:47082487-47082495 chr2:47082486-47082496 chr2:47082537-47082546 chr2:47082487-47082495 chr2:47082485-47082497 chr2:47082487-47082494
21	SP1	chr2:47081911-47083160	A549	lung:	n/a	chr2:47082701-47082715 chr2:47082694-47082708
22	JUND	chr2:47081996-47083816	SK-N-SH	brain:	n/a	chr2:47082538-47082546 chr2:47082538-47082545 chr2:47082537-47082547 chr2:47082536-47082548 chr2:47082487-47082495 chr2:47082486-47082496 chr2:47082537-47082546 chr2:47082487-47082495 chr2:47082485-47082497 chr2:47082536-47082547 chr2:47082487-47082494
23	MAX	chr2:47082019-47083223	HCT-116	colon:	n/a	chr2:47082487-47082496 chr2:47082537-47082546 chr2:47082693-47082703 chr2:47082538-47082547
24	REST	chr2:47081845-47083145	A549	lung:	n/a	chr2:47082714-47082723
25	TCF12	chr2:47081827-47083769	A549	lung:	n/a	chr2:47082192-47082202 chr2:47082699-47082709
26	MAZ	chr2:47081865-47083006	IMR90	lung:	n/a	chr2:47082487-47082496 chr2:47082537-47082546 chr2:47082693-47082703 chr2:47082538-47082547
27	GATA3	chr2:47081894-47083304	A549	lung:	n/a	chr2:47082669-47082679
28	EP300	chr2:47081547-47083239	SK-N-SH	brain:	n/a	chr2:47082487-47082496 chr2:47082537-47082546 chr2:47082262-47082276 chr2:47082538-47082547
29	EP300	chr2:47081964-47083218	SK-N-SH	brain:	n/a	chr2:47082487-47082496 chr2:47082537-47082546 chr2:47082262-47082276 chr2:47082538-47082547
30	POLR2A	chr2:47081988-47083097	U87	brain:	n/a	n/a
31	SP1	chr2:47081912-47083201	A549	lung:	n/a	chr2:47082701-47082715 chr2:47082694-47082708
32	FOXM1	chr2:47081672-47083124	SK-N-SH	brain:	n/a	n/a
33	GATA3	chr2:47081959-47083283	SK-N-SH	brain:	n/a	chr2:47082669-47082679

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:47072385..47074201-chr2:47081615..47083494,2	K562	blood:

Variant related genes	Relation type
ENSG00000226548	TF binding region
LINC01119	TF binding region
ENSG00000239332	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10170987	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10177555	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10177751	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10183609	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11125096	0.81[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11125097	0.83[ASN][1000 genomes]
rs11686200	0.83[MEX][hapmap]
rs11687883	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11689551	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2166478	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2278711	0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4953433	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9225	0.81[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs935372	0.81[CHD][hapmap];0.91[JPT][hapmap];0.96[MEX][hapmap];0.82[EUR][1000 genomes]
rs935379	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6759066	ABCG8	cis	parietal	SCAN
rs6759066	TTC7A	cis	cerebellum	SCAN
rs6759066	ATP6V1E2	cis	cerebellum	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47069400-47082400	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr2:47075200-47084400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:47077200-47086200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:47078000-47083400	Weak transcription	Fetal Intestine Large	intestine
5	chr2:47078000-47085200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr2:47078000-47085200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:47078400-47083200	Weak transcription	Psoas Muscle	Psoas
8	chr2:47078600-47082600	Weak transcription	Pancreas	Pancrea
9	chr2:47079200-47082600	Enhancers	HUVEC	blood vessel
10	chr2:47080600-47085000	Weak transcription	K562	blood
11	chr2:47080800-47084200	Enhancers	Left Ventricle	heart
12	chr2:47080800-47103600	Enhancers	Placenta	Placenta
13	chr2:47081000-47082200	Enhancers	Duodenum Smooth Muscle	Duodenum
14	chr2:47081200-47082200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr2:47081200-47082800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
16	chr2:47081200-47083800	Enhancers	Rectal Smooth Muscle	rectum
17	chr2:47081200-47087200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:47081400-47082200	Enhancers	NHEK	skin
19	chr2:47081400-47082600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:47081400-47082600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr2:47081400-47083000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:47081400-47083000	Enhancers	Adipose Nuclei	Adipose
23	chr2:47081400-47083200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr2:47081400-47083200	Enhancers	Fetal Muscle Leg	muscle
25	chr2:47081400-47083400	Enhancers	NHLF	lung
26	chr2:47081400-47083600	Enhancers	Fetal Stomach	stomach
27	chr2:47081400-47083800	Enhancers	Colon Smooth Muscle	Colon
28	chr2:47081400-47083800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr2:47081400-47083800	Enhancers	HSMMtube	muscle
30	chr2:47081400-47084000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:47081400-47086400	Enhancers	HMEC	breast
32	chr2:47081400-47086600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:47081400-47087200	Enhancers	Muscle Satellite Cultured Cells	--
34	chr2:47081400-47087800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:47081400-47091000	Enhancers	NHDF-Ad	bronchial
36	chr2:47081600-47082200	Enhancers	Aorta	Aorta
37	chr2:47081600-47082200	Enhancers	Brain Hippocampus Middle	brain
38	chr2:47081600-47082200	Enhancers	Colonic Mucosa	Colon
39	chr2:47081600-47082200	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr2:47081600-47082400	Enhancers	Brain Angular Gyrus	brain
41	chr2:47081600-47082400	Enhancers	Brain Anterior Caudate	brain
42	chr2:47081600-47082400	Enhancers	Right Ventricle	heart
43	chr2:47081600-47082800	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr2:47081600-47082800	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr2:47081600-47082800	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr2:47081600-47082800	Enhancers	Fetal Lung	lung
47	chr2:47081600-47082800	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr2:47081600-47083000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:47081600-47083400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:47081600-47083400	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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