Variant report

Variant	rs6966318
Chromosome Location	chr7:112092857-112092858
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	JUND	chr7:112092310-112092901	K562	blood:	n/a	n/a
2	RAD21	chr7:112092506-112092951	H1-hESC	embryonic stem cell:	n/a	chr7:112092732-112092751 chr7:112092735-112092748
3	SMC3	chr7:112092570-112092894	GM12878	blood:	n/a	chr7:112092736-112092750 chr7:112092743-112092750
4	CTCF	chr7:112092544-112092934	K562	blood:	n/a	chr7:112092740-112092749 chr7:112092736-112092749 chr7:112092729-112092750
5	POLR2A	chr7:112089448-112092907	HepG2	liver:	n/a	n/a
6	RAD21	chr7:112092498-112092882	HepG2	liver:	n/a	chr7:112092732-112092751 chr7:112092735-112092748
7	CTCF	chr7:112092720-112092870	HAc	cerebellar:	n/a	chr7:112092740-112092749 chr7:112092736-112092749 chr7:112092729-112092750
8	CHD1	chr7:112090507-112093089	H1-hESC	embryonic stem cell:	n/a	chr7:112091005-112091015
9	ZNF143	chr7:112092626-112092867	GM12878	blood:	n/a	n/a
10	MAFK	chr7:112092470-112092878	K562	blood:	n/a	n/a
11	MYC	chr7:112092397-112092910	MCF10A-Er-Src	breast:	n/a	chr7:112092799-112092808
12	EP300	chr7:112092622-112092898	K562	blood:	n/a	n/a
13	RAD21	chr7:112092556-112092896	Hela-S3	cervix:	n/a	chr7:112092732-112092751 chr7:112092735-112092748
14	CTCF	chr7:112092611-112092931	K562	blood:	n/a	chr7:112092740-112092749 chr7:112092736-112092749 chr7:112092729-112092750
15	ZC3H11A	chr7:112092321-112092900	K562	blood:	n/a	n/a
16	CTCF	chr7:112092554-112092860	K562	blood:	n/a	chr7:112092740-112092749 chr7:112092736-112092749 chr7:112092729-112092750
17	UBTF	chr7:112092258-112092899	K562	blood:	n/a	n/a
18	SMC3	chr7:112092654-112092888	K562	blood:	n/a	chr7:112092736-112092750 chr7:112092743-112092750
19	CTCF	chr7:112092720-112092870	HCM	heart:	n/a	chr7:112092740-112092749 chr7:112092736-112092749 chr7:112092729-112092750
20	NR2F2	chr7:112089740-112093055	K562	blood:	n/a	chr7:112092790-112092805
21	CTCF	chr7:112092760-112092910	HFF-Myc	foreskin:	n/a	n/a
22	RAD21	chr7:112092561-112092897	HepG2	liver:	n/a	chr7:112092732-112092751 chr7:112092735-112092748
23	RAD21	chr7:112092627-112092890	K562	blood:	n/a	chr7:112092732-112092751 chr7:112092735-112092748
24	CTCF	chr7:112092720-112092870	GM12870	blood:	n/a	chr7:112092740-112092749 chr7:112092736-112092749 chr7:112092729-112092750
25	ZNF143	chr7:112092593-112092882	K562	blood:	n/a	n/a
26	EP300	chr7:112092726-112092883	GM12878	blood:	n/a	n/a
27	RAD21	chr7:112092508-112092890	SK-N-SH_RA	brain:	n/a	chr7:112092732-112092751 chr7:112092735-112092748
28	STAT3	chr7:112092568-112093029	MCF10A-Er-Src	breast:	n/a	n/a
29	RCOR1	chr7:112092622-112092911	K562	blood:	n/a	n/a
30	POLR2A	chr7:112092697-112093115	MCF10A-Er-Src	breast:	n/a	n/a
31	ZNF263	chr7:112089981-112092890	HEK293-T-REx	kidney:	n/a	chr7:112090268-112090277 chr7:112092703-112092712
32	EBF1	chr7:112092263-112092862	GM12878	blood:	n/a	chr7:112092440-112092451
33	RAD21	chr7:112092444-112092881	H1-hESC	embryonic stem cell:	n/a	chr7:112092732-112092751 chr7:112092735-112092748
34	ARID3A	chr7:112092070-112093011	HepG2	liver:	n/a	n/a
35	POLR2A	chr7:112090070-112093219	K562	blood:	n/a	n/a
36	RAD21	chr7:112092571-112092871	H1-hESC	embryonic stem cell:	n/a	chr7:112092732-112092751 chr7:112092735-112092748
37	TBL1XR1	chr7:112092224-112092902	K562	blood:	n/a	n/a
38	MXI1	chr7:112092641-112092928	GM12878	blood:	n/a	n/a
39	RAD21	chr7:112092606-112092901	GM12878	blood:	n/a	chr7:112092732-112092751 chr7:112092735-112092748
40	POLR2A	chr7:112090230-112093056	A549	lung:	n/a	n/a
41	SMC3	chr7:112092617-112092860	HepG2	liver:	n/a	chr7:112092736-112092750 chr7:112092743-112092750
42	SMC3	chr7:112092229-112092898	Hela-S3	cervix:	n/a	chr7:112092736-112092750 chr7:112092743-112092750
43	POLR2A	chr7:112092301-112092986	HepG2	liver:	n/a	n/a
44	CTCF	chr7:112092740-112092890	GM12878	blood:	n/a	chr7:112092740-112092749
45	CTCF	chr7:112092519-112092940	GM12878	blood:	n/a	chr7:112092740-112092749 chr7:112092736-112092749 chr7:112092729-112092750
46	POLR2A	chr7:112089774-112093074	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr7:111977606..111981678-chr7:112089523..112092927,4	K562	blood:
2	chr7:112088943..112098465-chr7:112111106..112127214,31	K562	blood:
3	chr7:112089471..112094125-chr7:112120459..112123941,5	MCF-7	breast:
4	chr7:112088811..112094041-chr7:112100770..112110657,18	MCF-7	breast:
5	chr7:112088410..112092985-chr7:112428999..112431698,4	K562	blood:
6	chr7:112047884..112050486-chr7:112089235..112093334,4	MCF-7	breast:
7	chr7:112089375..112094700-chr7:112096975..112100569,9	MCF-7	breast:
8	chr7:112059129..112067568-chr7:112088387..112093703,18	K562	blood:
9	chr7:111806034..111807822-chr7:112092535..112095230,2	K562	blood:
10	chr1:24968714..24969624-chr7:112092230..112092922,2	Hela-S3	cervix:
11	chr7:112058803..112077296-chr7:112087519..112096464,50	MCF-7	breast:
12	chr7:112058693..112068099-chr7:112086961..112092875,22	MCF-7	breast:
13	chr7:112060645..112065287-chr7:112088150..112093147,11	K562	blood:

Variant related genes	Relation type
IFRD1	TF binding region
ENSG00000226851	Chromatin interaction
ENSG00000181016	Chromatin interaction
ENSG00000133226	Chromatin interaction
ENSG00000006652	Chromatin interaction
ENSG00000198839	Chromatin interaction
ENSG00000146802	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1468457	0.81[AFR][1000 genomes]
rs1468458	1.00[YRI][hapmap]
rs2074796	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2253962	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2529588	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2708606	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2708609	0.84[ASN][1000 genomes]
rs2708610	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs2708611	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3095025	0.89[ASN][1000 genomes]
rs3109112	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3128386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3128388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3183621	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3801795	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs3807213	1.00[LWK][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes]
rs4386904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6967593	1.00[LWK][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs7467	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.89[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	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	nsv831097	chr7:112000837-112113173	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer 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 target site	90 gene(s)	inside rSNPs	diseases
3	esv1801262	chr7:112071795-112104179	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	nsv1030033	chr7:112092709-112140430	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6966318	C7orf53	cis	brain	seeQTL
rs6966318	LSMEM1	cis	Thyroid	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112089600-112093000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr7:112089600-112093000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr7:112089600-112093400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr7:112089600-112094000	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr7:112089600-112094200	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr7:112089600-112094200	Active TSS	Psoas Muscle	Psoas
7	chr7:112089800-112093000	Active TSS	H1 Cell Line	embryonic stem cell
8	chr7:112089800-112093000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:112089800-112093000	Active TSS	Aorta	Aorta
10	chr7:112089800-112093000	Active TSS	Colon Smooth Muscle	Colon
11	chr7:112089800-112093000	Active TSS	Left Ventricle	heart
12	chr7:112089800-112093200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:112089800-112093400	Active TSS	A549	lung
14	chr7:112089800-112093600	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr7:112089800-112093600	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr7:112089800-112094400	Active TSS	Right Ventricle	heart
17	chr7:112089800-112094800	Active TSS	GM12878-XiMat	blood
18	chr7:112090000-112094600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:112090200-112093400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr7:112090200-112093400	Active TSS	HMEC	breast
21	chr7:112090200-112093400	Active TSS	HSMMtube	muscle
22	chr7:112090200-112094200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:112090400-112093000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr7:112091400-112093000	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr7:112091400-112093000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr7:112091400-112093000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr7:112091400-112093000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr7:112091400-112094000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr7:112091400-112094600	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr7:112091600-112093200	Active TSS	HepG2	liver
31	chr7:112091600-112093600	Flanking Active TSS	Primary hematopoietic stem cells	blood
32	chr7:112091600-112094400	Active TSS	Right Atrium	heart
33	chr7:112091800-112093000	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr7:112091800-112093000	Flanking Active TSS	Duodenum Mucosa	Duodenum
35	chr7:112091800-112093200	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr7:112091800-112093600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr7:112091800-112094000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
38	chr7:112091800-112094200	Flanking Active TSS	Dnd41	blood
39	chr7:112091800-112094600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr7:112092000-112093000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr7:112092000-112093000	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr7:112092000-112093200	Enhancers	Stomach Mucosa	stomach
43	chr7:112092000-112094400	Enhancers	Fetal Heart	heart
44	chr7:112092000-112094600	Enhancers	Small Intestine	intestine
45	chr7:112092200-112093000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr7:112092200-112093000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr7:112092200-112093000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
48	chr7:112092200-112093000	Flanking Active TSS	Rectal Smooth Muscle	rectum
49	chr7:112092200-112093200	Flanking Active TSS	Liver	Liver
50	chr7:112092200-112093200	Flanking Active TSS	Brain Hippocampus Middle	brain

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