Variant report

Variant	rs60924672
Chromosome Location	chr11:73098724-73098725
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:39)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:39 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:73098700-73098850	HFF	foreskin:	n/a	n/a
2	ESR1	chr11:73098608-73098968	ECC-1	luminal epithelium:	n/a	n/a
3	EP300	chr11:73098321-73099389	ECC-1	luminal epithelium:	n/a	n/a
4	MTA3	chr11:73098121-73099668	GM12878	blood:	n/a	n/a
5	CEBPB	chr11:73098555-73098814	IMR90	lung:	n/a	n/a
6	CTCF	chr11:73098720-73098870	GM12873	blood:	n/a	n/a
7	KAP1	chr11:73098454-73099059	U2OS	brain:	n/a	n/a
8	POLR2A	chr11:73098106-73111810	GM12878	blood:	n/a	n/a
9	EP300	chr11:73098517-73099115	ECC-1	luminal epithelium:	n/a	n/a
10	CTCF	chr11:73098720-73098870	GM12871	blood:	n/a	n/a
11	WRNIP1	chr11:73098416-73098791	GM12878	blood:	n/a	n/a
12	MAX	chr11:73098436-73099339	ECC-1	luminal epithelium:	n/a	chr11:73098681-73098690
13	MAX	chr11:73098166-73099143	NB4	blood:	n/a	chr11:73098681-73098690
14	KAP1	chr11:73098438-73099130	HEK293	kidney:	n/a	n/a
15	POLR2A	chr11:73098060-73100184	HL-60	blood:	n/a	n/a
16	EBF1	chr11:73098186-73098811	GM12878	blood:	n/a	n/a
17	CEBPB	chr11:73098527-73098855	Hela-S3	cervix:	n/a	n/a
18	SPI1	chr11:73097929-73098769	GM12878	blood:	n/a	n/a
19	CTCF	chr11:73098720-73098870	GM06990	blood:	n/a	n/a
20	TCF12	chr11:73098373-73099364	ECC-1	luminal epithelium:	n/a	chr11:73098572-73098579
21	POLR2A	chr11:73098540-73102525	A549	lung:	n/a	n/a
22	TCF12	chr11:73098441-73099373	ECC-1	luminal epithelium:	n/a	chr11:73098572-73098579
23	POLR2A	chr11:73098629-73098747	GM12878	blood:	n/a	n/a
24	CEBPB	chr11:73098508-73098885	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr11:73098107-73100258	HL-60	blood:	n/a	n/a
26	CTCF	chr11:73098680-73098830	HRPEpiC	eye:	n/a	n/a
27	ZBTB7A	chr11:73098253-73099017	ECC-1	luminal epithelium:	n/a	n/a
28	MAZ	chr11:73098273-73098774	GM12878	blood:	n/a	chr11:73098681-73098690
29	RUNX3	chr11:73098112-73099012	GM12878	blood:	n/a	n/a
30	ZBTB7A	chr11:73098432-73099148	ECC-1	luminal epithelium:	n/a	n/a
31	CTCF	chr11:73098720-73098870	HRPEpiC	eye:	n/a	n/a
32	ELF1	chr11:73098493-73099340	GM12878	blood:	n/a	n/a
33	CEBPB	chr11:73098443-73099067	ECC-1	luminal epithelium:	n/a	n/a
34	CTCF	chr11:73098700-73098850	HPF	lung:	n/a	n/a
35	NFIC	chr11:73098371-73099272	ECC-1	luminal epithelium:	n/a	n/a
36	MAX	chr11:73098487-73099528	ECC-1	luminal epithelium:	n/a	chr11:73098681-73098690
37	STAT5A	chr11:73098382-73099408	GM12878	blood:	n/a	chr11:73099037-73099044
38	NFIC	chr11:73098401-73099306	ECC-1	luminal epithelium:	n/a	n/a
39	ZNF263	chr11:73098557-73100000	HEK293-T-REx	kidney:	n/a	chr11:73099713-73099722 chr11:73099482-73099491

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:73017324..73020653-chr11:73098598..73101937,4	MCF-7	breast:
2	chr11:73097268..73098971-chr11:73100387..73103258,2	MCF-7	breast:
3	chr11:73098600..73102285-chr11:73102322..73106479,4	MCF-7	breast:
4	chr11:73066533..73068144-chr11:73097235..73098913,2	K562	blood:
5	chr11:73061043..73065254-chr11:73095025..73099626,5	MCF-7	breast:
6	chr11:73064939..73068033-chr11:73095872..73098913,3	K562	blood:

No data

Variant related genes	Relation type
RELT	TF binding region
ENSG00000110237	Chromatin interaction
ENSG00000257038	Chromatin interaction
ENSG00000054967	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1002127	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10898917	0.85[EUR][1000 genomes]
rs11544310	1.00[ASN][1000 genomes]
rs11544311	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12099129	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17244596	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17244602	0.83[AMR][1000 genomes]
rs28400367	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741149	0.81[EUR][1000 genomes]
rs3741151	0.81[EUR][1000 genomes]
rs56742470	0.83[AMR][1000 genomes]
rs57354084	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs58334887	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58564192	0.83[AMR][1000 genomes]
rs61345051	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6592526	0.91[AMR][1000 genomes]
rs7110369	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7112924	1.00[ASN][1000 genomes]
rs7115055	0.83[AMR][1000 genomes]
rs7129546	0.83[AMR][1000 genomes]
rs7129663	0.81[EUR][1000 genomes]
rs73542929	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542938	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542952	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542960	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542967	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542976	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542979	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73542990	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73543000	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73544710	0.85[EUR][1000 genomes]
rs73544711	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73544716	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73544720	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73544729	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73544767	0.91[AMR][1000 genomes]
rs73544783	0.83[AMR][1000 genomes]
rs7925226	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7930880	0.80[EUR][1000 genomes]
rs7941454	0.87[EUR][1000 genomes]
rs7951072	0.83[AMR][1000 genomes]
rs7951174	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821041	chr11:72937162-73113080	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv897911	chr11:73044351-73108276	Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	esv3395161	chr11:73084616-73461577	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60924672	ARHGEF17	cis	Whole Blood	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:73088400-73100200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr11:73088600-73100800	Enhancers	Placenta	Placenta
3	chr11:73089000-73099600	Enhancers	A549	lung
4	chr11:73089000-73100600	Enhancers	Fetal Muscle Leg	muscle
5	chr11:73089000-73101000	Enhancers	Brain Hippocampus Middle	brain
6	chr11:73090000-73101400	Enhancers	Adipose Nuclei	Adipose
7	chr11:73090600-73099600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr11:73091000-73104200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr11:73091200-73100200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
10	chr11:73091400-73100200	Enhancers	Fetal Thymus	thymus
11	chr11:73091600-73101600	Enhancers	Fetal Muscle Trunk	muscle
12	chr11:73092400-73099600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr11:73092600-73099000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr11:73092600-73100800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr11:73093000-73099400	Enhancers	Duodenum Mucosa	Duodenum
16	chr11:73093000-73099600	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr11:73093200-73099000	Enhancers	NHEK	skin
18	chr11:73093200-73099600	Enhancers	Thymus	Thymus
19	chr11:73093600-73099200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr11:73093600-73099800	Enhancers	Primary T cells from cord blood	blood
21	chr11:73094000-73099200	Enhancers	Primary T killer memory cells from peripheral blood	blood
22	chr11:73095000-73099400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr11:73095000-73103400	Weak transcription	Gastric	stomach
24	chr11:73095200-73100000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr11:73095200-73116200	Weak transcription	Liver	Liver
26	chr11:73095400-73103000	Weak transcription	NHLF	lung
27	chr11:73095600-73099600	Weak transcription	Pancreas	Pancrea
28	chr11:73095800-73099000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr11:73095800-73099000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr11:73095800-73100000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr11:73095800-73100200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:73096000-73099200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr11:73096000-73099800	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr11:73096000-73100400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr11:73096200-73098800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr11:73096200-73099000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr11:73096200-73099600	Enhancers	Fetal Lung	lung
38	chr11:73096200-73101800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr11:73096200-73130200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr11:73096400-73099000	Weak transcription	Esophagus	oesophagus
41	chr11:73096400-73099200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:73096400-73099400	Flanking Active TSS	Primary B cells from cord blood	blood
43	chr11:73096400-73100000	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr11:73096600-73099000	Weak transcription	Left Ventricle	heart
45	chr11:73096600-73100200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:73096600-73104400	Weak transcription	Fetal Brain Male	brain
47	chr11:73096800-73098800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr11:73096800-73098800	Enhancers	Fetal Brain Female	brain
49	chr11:73096800-73099000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
50	chr11:73096800-73099800	Enhancers	ES-I3 Cell Line	embryonic stem cell

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