Variant report

Variant	rs7479407
Chromosome Location	chr11:9023421-9023422
allele	A/G
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	POLR2A	chr11:9023307-9023786	U87	brain:	n/a	n/a
2	MYC	chr11:9023326-9023821	MCF10A-Er-Src	breast:	n/a	n/a
3	ARID3A	chr11:9023362-9023600	K562	blood:	n/a	n/a
4	POLR2A	chr11:9023184-9023807	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr11:9023420-9023429	Gliobla	brain:	n/a	n/a
6	CUX1	chr11:9023043-9023931	K562	blood:	n/a	n/a
7	FOS	chr11:9023273-9023748	MCF10A-Er-Src	breast:	n/a	chr11:9023566-9023574 chr11:9023564-9023575
8	MAX	chr11:9023301-9023616	K562	blood:	n/a	n/a
9	RCOR1	chr11:9023371-9023614	K562	blood:	n/a	n/a
10	CBX3	chr11:9023224-9023690	K562	blood:	n/a	n/a
11	FOS	chr11:9023279-9023724	MCF10A-Er-Src	breast:	n/a	chr11:9023566-9023574 chr11:9023564-9023575
12	ATF3	chr11:9023268-9023700	K562	blood:	n/a	n/a
13	MYC	chr11:9023337-9023630	HUVEC	blood vessel:	n/a	n/a
14	E2F6	chr11:9023232-9023548	K562	blood:	n/a	n/a
15	UBTF	chr11:9023373-9023706	K562	blood:	n/a	n/a
16	MXI1	chr11:9022752-9023898	IMR90	lung:	n/a	n/a
17	ELF1	chr11:9023275-9023714	K562	blood:	n/a	n/a
18	BHLHE40	chr11:9023304-9023690	K562	blood:	n/a	n/a
19	JUN	chr11:9023027-9024210	K562	blood:	n/a	chr11:9023566-9023574
20	STAT3	chr11:9023271-9023744	MCF10A-Er-Src	breast:	n/a	n/a
21	FOS	chr11:9023259-9023755	MCF10A-Er-Src	breast:	n/a	chr11:9023566-9023574 chr11:9023564-9023575
22	E2F6	chr11:9023220-9023601	K562	blood:	n/a	n/a
23	MAX	chr11:9023259-9023577	K562	blood:	n/a	n/a
24	FOSL1	chr11:9023212-9023709	K562	blood:	n/a	chr11:9023566-9023574
25	EP300	chr11:9023313-9023938	K562	blood:	n/a	chr11:9023873-9023887 chr11:9023480-9023487 chr11:9023754-9023763 chr11:9023647-9023656
26	JUND	chr11:9023311-9023703	K562	blood:	n/a	chr11:9023566-9023574
27	MAX	chr11:9023257-9023689	HCT-116	colon:	n/a	n/a
28	MAX	chr11:9023249-9023715	NB4	blood:	n/a	n/a
29	MYC	chr11:9023302-9023678	NB4	blood:	n/a	n/a
30	TEAD4	chr11:9023237-9024023	K562	blood:	n/a	n/a
31	E2F4	chr11:9023273-9023689	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr11:9023395-9023621	MCF10A-Er-Src	breast:	n/a	chr11:9023566-9023574 chr11:9023564-9023575
33	MAFK	chr11:9023340-9023649	IMR90	lung:	n/a	n/a
34	MAFK	chr11:9023338-9023681	K562	blood:	n/a	n/a
35	CEBPB	chr11:9023293-9023705	IMR90	lung:	n/a	n/a
36	STAT3	chr11:9023297-9023858	MCF10A-Er-Src	breast:	n/a	chr11:9023778-9023792
37	MAX	chr11:9023257-9023730	SK-N-SH	brain:	n/a	n/a
38	YY1	chr11:9023323-9023629	K562	blood:	n/a	n/a
39	MYC	chr11:9023373-9023628	K562	blood:	n/a	n/a
40	JUN	chr11:9023295-9023678	HUVEC	blood vessel:	n/a	chr11:9023566-9023574
41	STAT3	chr11:9023284-9023616	MCF10A-Er-Src	breast:	n/a	n/a
42	POLR2A	chr11:9023337-9023610	HUVEC	blood vessel:	n/a	n/a
43	MAX	chr11:9023197-9023685	K562	blood:	n/a	n/a
44	HMGN3	chr11:9023361-9023669	K562	blood:	n/a	n/a
45	ATF1	chr11:9023290-9023698	K562	blood:	n/a	n/a
46	RAD21	chr11:9023363-9023746	IMR90	lung:	n/a	n/a
47	FOS	chr11:9023205-9023790	HUVEC	blood vessel:	n/a	chr11:9023566-9023574 chr11:9023564-9023575

No.	Distal block	Cell Line	Cell type
1	chr11:9022966..9025427-chr11:9154942..9157918,2	K562	blood:
2	chr11:9020957..9023609-chr11:9034116..9037224,3	K562	blood:
3	chr11:9023067..9025427-chr11:9156418..9158861,2	K562	blood:
4	chr11:8996724..8999605-chr11:9022687..9025353,2	K562	blood:

Variant related genes	Relation type
ENSG00000253973	TF binding region

Extended variants
information (count: 77 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10743093	0.92[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap]
rs10743095	0.84[EUR][1000 genomes]
rs10769967	0.93[CEU][hapmap]
rs10769970	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10769971	0.87[JPT][hapmap]
rs10769973	0.93[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap]
rs10769978	0.85[EUR][1000 genomes]
rs10769979	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769980	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10769981	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10840130	0.84[CEU][hapmap]
rs10840134	0.92[CEU][hapmap];0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10840141	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10840142	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs10840147	0.89[ASW][hapmap];0.89[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs10840148	1.00[ASW][hapmap];0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap]
rs10840157	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10840158	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10840160	0.86[MEX][hapmap];0.92[TSI][hapmap]
rs11042078	0.89[CEU][hapmap]
rs11042103	0.93[CEU][hapmap];0.83[CHB][hapmap];0.86[JPT][hapmap]
rs11042125	0.89[ASW][hapmap];0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11042149	0.89[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs11042150	0.82[EUR][1000 genomes]
rs11042151	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs11042152	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11042154	1.00[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1109305	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1123936	0.93[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs11603841	0.88[CEU][hapmap]
rs1529641	0.91[CEU][hapmap]
rs1560569	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs1980428	0.93[CEU][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs1980429	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1984791	0.83[CHB][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[ASN][1000 genomes]
rs2012680	0.95[ASN][1000 genomes]
rs2012690	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2012696	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2016942	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2568020	0.96[ASN][1000 genomes]
rs2568043	0.92[CEU][hapmap]
rs2568045	0.93[CEU][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs2568061	0.93[CEU][hapmap];0.91[MEX][hapmap]
rs2568065	0.93[CEU][hapmap];0.91[MEX][hapmap]
rs2568090	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs2653570	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.96[ASN][1000 genomes]
rs2653605	0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.96[ASN][1000 genomes]
rs2742470	0.82[EUR][1000 genomes]
rs2742471	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742474	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2742480	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2742537	0.83[CEU][hapmap]
rs2742540	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs2742545	0.85[CEU][hapmap]
rs2742552	0.85[CEU][hapmap];0.87[MEX][hapmap]
rs4909952	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4910062	0.92[CEU][hapmap];0.80[JPT][hapmap]
rs4910156	0.84[EUR][1000 genomes]
rs4910158	0.83[EUR][1000 genomes]
rs4910200	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4910442	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs4929922	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6486060	0.92[CEU][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs7119939	0.92[CEU][hapmap]
rs7123429	0.93[CEU][hapmap]
rs7482838	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7484180	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7925728	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7930026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7937298	0.93[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap]
rs7945705	0.93[CEU][hapmap];0.82[JPT][hapmap];0.82[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv896984	chr11:8988550-9090408	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
5	esv3477864	chr11:9023195-9023500	Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3477875	chr11:9023270-9023428	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs7479407	TMEM9B-AS1	cis	lung	GTEx
rs7479407	AKIP1	cis	Thyroid	GTEx
rs7479407	ST5	cis	parietal	SCAN
rs7479407	RPL27A	cis	parietal	SCAN
rs7479407	NRIP3	cis	parietal	SCAN
rs7479407	WEE1	cis	parietal	SCAN
rs7479407	APBB1	cis	parietal	SCAN
rs7479407	RRP8	cis	parietal	SCAN
rs7479407	C11orf17	cis	multi-tissue	Pritchard
rs7479407	OR52A1	cis	parietal	SCAN
rs7479407	TMEM9B	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9022600-9024600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr11:9022800-9023600	Enhancers	Monocytes-CD14+_RO01746	blood
3	chr11:9022800-9024400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr11:9022800-9024600	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr11:9023000-9023600	Flanking Active TSS	K562	blood
6	chr11:9023000-9023600	Enhancers	NHLF	lung
7	chr11:9023000-9023800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
8	chr11:9023000-9024200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:9023000-9024400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr11:9023000-9024400	Enhancers	Osteobl	bone
11	chr11:9023000-9024600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:9023000-9024600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr11:9023200-9023600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr11:9023200-9023600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:9023200-9023600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr11:9023200-9023600	ZNF genes & repeats	Pancreas	Pancrea
17	chr11:9023200-9023600	Enhancers	Hela-S3	cervix
18	chr11:9023200-9023600	Enhancers	NH-A	brain
19	chr11:9023200-9023600	Flanking Active TSS	NHDF-Ad	bronchial
20	chr11:9023200-9023800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr11:9023200-9024000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
22	chr11:9023200-9024200	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:9023200-9024200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr11:9023200-9024400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr11:9023200-9024400	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
26	chr11:9023200-9024400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr11:9023200-9024600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:9023200-9024600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
29	chr11:9023200-9024600	Enhancers	Muscle Satellite Cultured Cells	--
30	chr11:9023200-9024600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr11:9023200-9024600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr11:9023200-9024600	Enhancers	HMEC	breast
33	chr11:9023200-9024600	Enhancers	HSMM	muscle
34	chr11:9023200-9024600	Enhancers	HUVEC	blood vessel
35	chr11:9023200-9024600	Enhancers	NHEK	skin
36	chr11:9023200-9025000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:9023400-9023600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
38	chr11:9023400-9023600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr11:9023400-9023600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
40	chr11:9023400-9023600	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
41	chr11:9023400-9023600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
42	chr11:9023400-9023600	Bivalent Enhancer	Brain Germinal Matrix	brain
43	chr11:9023400-9023600	Enhancers	Gastric	stomach
44	chr11:9023400-9023600	Enhancers	Spleen	Spleen
45	chr11:9023400-9023800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
46	chr11:9023400-9023800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr11:9023400-9024600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr11:9023400-9024800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
49	chr11:9023400-9024800	Bivalent Enhancer	Fetal Thymus	thymus

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