Variant report

Variant	rs6967593
Chromosome Location	chr7:112096792-112096793
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	RFX5	chr7:112096694-112096828	K562	blood:	n/a	n/a
2	JUND	chr7:112096707-112096907	HepG2	liver:	n/a	chr7:112096794-112096805 chr7:112096795-112096804 chr7:112096797-112096804 chr7:112096891-112096900
3	FOS	chr7:112096618-112096873	MCF10A-Er-Src	breast:	n/a	chr7:112096795-112096804 chr7:112096797-112096804
4	FOS	chr7:112096653-112096891	MCF10A-Er-Src	breast:	n/a	chr7:112096795-112096804 chr7:112096797-112096804
5	TCF7L2	chr7:112096605-112096868	HepG2	liver:	n/a	chr7:112096795-112096804

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:112088943..112098465-chr7:112111106..112127214,31	K562	blood:
2	chr7:112096348..112097855-chr7:112118950..112121357,2	MCF-7	breast:

Variant related genes	Relation type
IFRD1	TF binding region
ENSG00000181016	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs1005659	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1005661	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1024568	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1024569	0.92[ASN][1000 genomes]
rs1024570	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1024572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10260414	0.92[ASN][1000 genomes]
rs1029631	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10500007	1.00[CHB][hapmap];0.89[JPT][hapmap];0.99[ASN][1000 genomes]
rs1054043	0.92[ASN][1000 genomes]
rs10953712	0.91[ASN][1000 genomes]
rs10953713	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11514940	0.92[ASN][1000 genomes]
rs11764489	0.93[ASN][1000 genomes]
rs11769604	0.91[ASN][1000 genomes]
rs12154294	0.92[ASN][1000 genomes]
rs12531101	0.94[ASN][1000 genomes]
rs12531636	0.94[ASN][1000 genomes]
rs12539263	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1468457	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1468458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17159684	0.97[ASN][1000 genomes]
rs17159686	1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1963308	0.92[ASN][1000 genomes]
rs2074796	0.81[ASW][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2190587	0.92[ASN][1000 genomes]
rs2253962	1.00[LWK][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs2396541	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2396542	0.92[ASN][1000 genomes]
rs2708611	0.91[YRI][hapmap];0.88[AFR][1000 genomes]
rs3095035	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3128386	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs3128388	0.91[YRI][hapmap];0.90[AFR][1000 genomes]
rs34633971	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36095669	0.92[ASN][1000 genomes]
rs3807206	0.92[ASN][1000 genomes]
rs3807210	0.92[ASN][1000 genomes]
rs3807213	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[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4275157	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs4386904	0.87[YRI][hapmap];0.90[AFR][1000 genomes]
rs4727771	0.99[ASN][1000 genomes]
rs4727774	0.92[ASN][1000 genomes]
rs4730548	0.99[ASN][1000 genomes]
rs4730549	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs55954386	1.00[ASN][1000 genomes]
rs56020731	0.99[ASN][1000 genomes]
rs6944364	1.00[CHB][hapmap];0.92[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs6945176	0.92[CHB][hapmap];0.89[JPT][hapmap];1.00[ASN][1000 genomes]
rs6963343	0.86[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.85[ASN][1000 genomes]
rs6966318	1.00[LWK][hapmap];0.89[MKK][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes]
rs6967894	1.00[ASN][1000 genomes]
rs6968084	1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6973615	0.92[ASN][1000 genomes]
rs73201469	0.92[ASN][1000 genomes]
rs7455170	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7467	0.81[ASW][hapmap];0.97[LWK][hapmap];0.94[MKK][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs7777925	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7817	1.00[CHB][hapmap];1.00[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.92[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs6967593	IFRD1	cis	parietal	SCAN
rs6967593	C7orf53	cis	parietal	SCAN
rs6967593	IFRD1	cis	Esophagus Mucosa	GTEx
rs6967593	LSMEM1	cis	Thyroid	GTEx
rs6967593	IFRD1	Cis_1M	lymphoblastoid	RTeQTL
rs6967593	IFRD1	cis	multi-tissue	Pritchard
rs6967593	IFRD1	cis	Thyroid	GTEx
rs6967593	IFRD1	cis	brain	BrainEAC
rs6967593	C7orf53	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112092600-112098800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr7:112092600-112099000	Weak transcription	Spleen	Spleen
3	chr7:112092600-112099800	Weak transcription	Esophagus	oesophagus
4	chr7:112092600-112099800	Weak transcription	Gastric	stomach
5	chr7:112092600-112102400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr7:112092600-112109800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:112092600-112121800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr7:112092800-112097000	Weak transcription	Colonic Mucosa	Colon
9	chr7:112093000-112098800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:112093000-112099800	Weak transcription	Thymus	Thymus
11	chr7:112093000-112109600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr7:112093200-112097200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr7:112093400-112096800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr7:112093800-112097000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr7:112093800-112097000	Weak transcription	Fetal Brain Female	brain
16	chr7:112093800-112098600	Weak transcription	Primary T cells from cord blood	blood
17	chr7:112094000-112102200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr7:112094000-112118200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr7:112094000-112121400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr7:112094400-112098800	Weak transcription	Fetal Stomach	stomach
21	chr7:112094400-112100400	Weak transcription	Fetal Heart	heart
22	chr7:112094400-112118200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr7:112094600-112098800	Weak transcription	Fetal Intestine Small	intestine
24	chr7:112094600-112098800	Weak transcription	Psoas Muscle	Psoas
25	chr7:112094600-112099000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr7:112094600-112102200	Weak transcription	Fetal Brain Male	brain
27	chr7:112094600-112105200	Strong transcription	K562	blood
28	chr7:112094600-112109800	Weak transcription	Small Intestine	intestine
29	chr7:112094600-112114800	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr7:112094600-112117000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr7:112094800-112097600	Weak transcription	Rectal Smooth Muscle	rectum
32	chr7:112094800-112098800	Weak transcription	Aorta	Aorta
33	chr7:112094800-112101600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr7:112095000-112100800	Strong transcription	Primary neutrophils fromperipheralblood	blood
35	chr7:112095000-112100800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr7:112095000-112114200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr7:112095200-112098800	Weak transcription	Left Ventricle	heart
38	chr7:112095200-112098800	Weak transcription	Lung	lung
39	chr7:112095200-112099400	Strong transcription	NHEK	skin
40	chr7:112095200-112109800	Weak transcription	Right Ventricle	heart
41	chr7:112095200-112117400	Strong transcription	HUES64 Cell Line	embryonic stem cell
42	chr7:112095400-112105200	Strong transcription	Fetal Muscle Trunk	muscle
43	chr7:112095400-112108000	Strong transcription	Fetal Intestine Large	intestine
44	chr7:112095400-112117200	Strong transcription	Dnd41	blood
45	chr7:112095600-112097400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr7:112095600-112097400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
47	chr7:112095600-112098800	Weak transcription	Pancreas	Pancrea
48	chr7:112095600-112101200	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr7:112095600-112101600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr7:112095600-112102000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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