Variant report

Variant	rs1632854
Chromosome Location	chr6:30975649-30975650
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	FOS	chr6:30975415-30975895	MCF10A-Er-Src	breast:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
2	SIN3AK20	chr6:30975429-30976039	SK-N-SH	brain:	n/a	n/a
3	EP300	chr6:30975289-30976181	SK-N-SH	brain:	n/a	chr6:30975612-30975621 chr6:30975577-30975587
4	GATA3	chr6:30975309-30976137	SK-N-SH	brain:	n/a	chr6:30975659-30975666 chr6:30975613-30975622
5	KAP1	chr6:30975380-30975881	U2OS	brain:	n/a	n/a
6	PBX3	chr6:30975360-30976074	SK-N-SH	brain:	n/a	n/a
7	NFIC	chr6:30975316-30976200	SK-N-SH	brain:	n/a	n/a
8	GATA3	chr6:30975288-30976162	SK-N-SH	brain:	n/a	chr6:30975659-30975666 chr6:30975613-30975622
9	TCF12	chr6:30975274-30976176	SK-N-SH	brain:	n/a	chr6:30975501-30975509
10	MAX	chr6:30975381-30976312	SK-N-SH	brain:	n/a	n/a
11	MAFK	chr6:30975415-30975875	IMR90	lung:	n/a	n/a
12	FOSL2	chr6:30975387-30975891	A549	lung:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
13	EP300	chr6:30975467-30975887	SK-N-SH_RA	brain:	n/a	chr6:30975612-30975621 chr6:30975577-30975587
14	JUND	chr6:30975347-30975962	HCT-116	colon:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
15	PBX3	chr6:30975325-30976122	SK-N-SH	brain:	n/a	n/a
16	JUND	chr6:30975277-30976015	SK-N-SH	brain:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
17	FOSL2	chr6:30975374-30975915	SK-N-SH	brain:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
18	E2F4	chr6:30975579-30975825	MCF10A-Er-Src	breast:	n/a	chr6:30975695-30975709
19	RCOR1	chr6:30975065-30976239	IMR90	lung:	n/a	n/a
20	JUND	chr6:30975386-30975953	HCT-116	colon:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
21	ELF1	chr6:30975416-30976101	SK-N-SH	brain:	n/a	n/a
22	FOS	chr6:30975441-30975872	MCF10A-Er-Src	breast:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
23	FOSL1	chr6:30975351-30975996	HCT-116	colon:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
24	FOSL2	chr6:30975366-30975817	MCF-7	breast:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
25	POLR2A	chr6:30975386-30975995	SK-N-SH	brain:	n/a	n/a
26	TEAD4	chr6:30975382-30976108	SK-N-SH	brain:	n/a	n/a
27	RXRA	chr6:30975224-30976089	SK-N-SH	brain:	n/a	n/a
28	TCF12	chr6:30975255-30976393	SK-N-SH	brain:	n/a	chr6:30975501-30975509
29	FOS	chr6:30975445-30975838	MCF10A-Er-Src	breast:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
30	FOSL2	chr6:30975359-30976326	SK-N-SH	brain:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
31	STAT3	chr6:30975485-30975895	MCF10A-Er-Src	breast:	n/a	n/a
32	MYC	chr6:30975545-30975813	MCF10A-Er-Src	breast:	n/a	n/a
33	RAD21	chr6:30975465-30975846	SK-N-SH_RA	brain:	n/a	n/a
34	JUND	chr6:30975477-30975955	MCF-7	breast:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
35	RAD21	chr6:30975530-30975852	SK-N-SH_RA	brain:	n/a	n/a
36	EP300	chr6:30975462-30975899	SK-N-SH_RA	brain:	n/a	chr6:30975612-30975621 chr6:30975577-30975587
37	FOS	chr6:30975436-30975892	MCF10A-Er-Src	breast:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
38	JUND	chr6:30975264-30976315	SK-N-SH	brain:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
39	STAT3	chr6:30975448-30975894	MCF10A-Er-Src	breast:	n/a	n/a
40	RUNX3	chr6:30975338-30975898	GM12878	blood:	n/a	chr6:30975770-30975779 chr6:30975770-30975779
41	STAT3	chr6:30975343-30975910	MCF10A-Er-Src	breast:	n/a	n/a
42	JUND	chr6:30975247-30976109	SK-N-SH	brain:	n/a	chr6:30975611-30975622 chr6:30975612-30975620 chr6:30975612-30975620 chr6:30975612-30975619
43	MAX	chr6:30975402-30975977	SK-N-SH	brain:	n/a	n/a
44	EP300	chr6:30975328-30976164	SK-N-SH	brain:	n/a	chr6:30975612-30975621 chr6:30975577-30975587

No.	Distal block	Cell Line	Cell type
1	chr6:30966029..30968135-chr6:30974071..30975905,2	MCF-7	breast:
2	chr6:26157901..26159583-chr6:30975186..30977903,2	K562	blood:
3	chr6:30967966..30971967-chr6:30974378..30977539,3	K562	blood:
4	chr6:30954105..30955673-chr6:30975592..30977694,2	K562	blood:

Variant related genes	Relation type
MUC22	TF binding region
ENSG00000158373	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1632862	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1634717	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	esv3358044	chr6:30940552-31000175	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1023108	chr6:30944982-30990490	Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv462745	chr6:30955681-30987176	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
9	nsv601485	chr6:30955681-30987176	Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv601486	chr6:30957618-30980015	Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv970676	chr6:30966672-30987268	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
12	nsv601487	chr6:30972589-30991559	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1632854	OR2B6	cis	parietal	SCAN
rs1632854	ZKSCAN4	cis	cerebellum	SCAN
rs1632854	ZNF391	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30965200-30975800	Weak transcription	Gastric	stomach
2	chr6:30970600-30978000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:30972600-30997600	Weak transcription	Right Atrium	heart
4	chr6:30973400-30976000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:30974000-30976200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:30975000-30976000	Enhancers	NHLF	lung
7	chr6:30975000-30976200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:30975000-30976200	Enhancers	HSMMtube	muscle
9	chr6:30975000-30976200	Enhancers	NH-A	brain
10	chr6:30975000-30976400	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr6:30975000-30976400	Enhancers	Placenta Amnion	Placenta Amnion
12	chr6:30975000-30976400	Enhancers	HMEC	breast
13	chr6:30975000-30976400	Enhancers	HSMM	muscle
14	chr6:30975000-30976400	Enhancers	NHDF-Ad	bronchial
15	chr6:30975000-30979400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr6:30975200-30975800	Enhancers	Osteobl	bone
17	chr6:30975200-30976200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr6:30975200-30976200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
19	chr6:30975200-30976200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:30975200-30976200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr6:30975200-30976200	Enhancers	NHEK	skin
22	chr6:30975200-30976400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr6:30975400-30975800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:30975400-30976000	Bivalent Enhancer	HepG2	liver
25	chr6:30975400-30976200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr6:30975400-30976200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:30975400-30976400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:30975400-30976400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:30975600-30975800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:30975600-30976000	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr6:30975600-30976000	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr6:30975600-30976200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:30975600-30976200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr6:30975600-30976200	Enhancers	Brain Anterior Caudate	brain
35	chr6:30975600-30976200	Enhancers	Brain Cingulate Gyrus	brain
36	chr6:30975600-30976200	Enhancers	Brain Substantia Nigra	brain
37	chr6:30975600-30976200	Enhancers	A549	lung

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