Variant report

Variant	rs11211420
Chromosome Location	chr1:47497037-47497038
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	FOXA1	chr1:47496767-47497073	HepG2	liver:	n/a	chr1:47496856-47496871
2	KAP1	chr1:47496622-47497509	U2OS	brain:	n/a	n/a
3	SIN3AK20	chr1:47496513-47497126	MCF-7	breast:	n/a	n/a
4	ESR1	chr1:47496642-47497041	T-47D	breast:	n/a	n/a
5	FOS	chr1:47496748-47497514	HUVEC	blood vessel:	n/a	n/a
6	TCF7L2	chr1:47496688-47497095	MCF-7	breast:	n/a	n/a
7	STAT3	chr1:47496583-47497104	MCF10A-Er-Src	breast:	n/a	n/a
8	GATA3	chr1:47496647-47497079	MCF-7	breast:	n/a	chr1:47496971-47496981
9	FOS	chr1:47496016-47497620	MCF10A-Er-Src	breast:	n/a	chr1:47496302-47496311 chr1:47496302-47496312 chr1:47496304-47496311 chr1:47496303-47496312 chr1:47496301-47496313 chr1:47496303-47496311 chr1:47496301-47496312
10	STAT3	chr1:47496207-47497510	MCF10A-Er-Src	breast:	n/a	chr1:47496302-47496311 chr1:47496303-47496312 chr1:47497332-47497340
11	ESR1	chr1:47496713-47497050	T-47D	breast:	n/a	n/a
12	FOXA1	chr1:47496719-47497080	A549	lung:	n/a	chr1:47496856-47496871
13	GATA3	chr1:47496503-47497177	MCF-7	breast:	n/a	chr1:47496971-47496981
14	FOXA2	chr1:47496638-47497052	A549	lung:	n/a	n/a
15	GATA3	chr1:47496633-47497096	T-47D	breast:	n/a	chr1:47496971-47496981
16	ZNF217	chr1:47496643-47497178	MCF-7	breast:	n/a	n/a
17	GATA3	chr1:47496620-47497085	T-47D	breast:	n/a	chr1:47496971-47496981
18	NR3C1	chr1:47496711-47497053	A549	lung:	n/a	chr1:47496827-47496853 chr1:47496831-47496849 chr1:47496840-47496847 chr1:47496827-47496853 chr1:47496899-47496925
19	POLR2A	chr1:47495980-47497079	MCF10A-Er-Src	breast:	n/a	n/a
20	SIN3AK20	chr1:47496377-47497335	MCF-7	breast:	n/a	n/a
21	GATA3	chr1:47496766-47497149	MCF-7	breast:	n/a	chr1:47496971-47496981
22	NR2F2	chr1:47496500-47497165	MCF-7	breast:	n/a	n/a
23	KAP1	chr1:47496663-47497326	HEK293	kidney:	n/a	n/a
24	STAT3	chr1:47495839-47497619	MCF10A-Er-Src	breast:	n/a	chr1:47496302-47496311 chr1:47496303-47496312 chr1:47497332-47497340
25	TCF7L2	chr1:47496819-47497071	PANC-1	pancreas:	n/a	n/a
26	E2F4	chr1:47496815-47497060	MCF10A-Er-Src	breast:	n/a	n/a
27	EP300	chr1:47496644-47497159	MCF-7	breast:	n/a	chr1:47496970-47496979
28	HDAC2	chr1:47496578-47497067	MCF-7	breast:	n/a	n/a
29	FOS	chr1:47495862-47497618	MCF10A-Er-Src	breast:	n/a	chr1:47496302-47496311 chr1:47496302-47496312 chr1:47496304-47496311 chr1:47496303-47496312 chr1:47496301-47496313 chr1:47496303-47496311 chr1:47496301-47496312
30	ESR1	chr1:47496642-47497098	T-47D	breast:	n/a	n/a
31	STAT3	chr1:47496645-47497256	MCF10A-Er-Src	breast:	n/a	n/a
32	FOS	chr1:47496042-47497616	MCF10A-Er-Src	breast:	n/a	chr1:47496302-47496311 chr1:47496302-47496312 chr1:47496304-47496311 chr1:47496303-47496312 chr1:47496301-47496313 chr1:47496303-47496311 chr1:47496301-47496312
33	MYC	chr1:47496642-47497107	MCF10A-Er-Src	breast:	n/a	n/a
34	MYC	chr1:47496701-47497165	MCF10A-Er-Src	breast:	n/a	n/a
35	FOS	chr1:47496142-47497054	MCF10A-Er-Src	breast:	n/a	chr1:47496302-47496311 chr1:47496302-47496312 chr1:47496304-47496311 chr1:47496303-47496312 chr1:47496301-47496313 chr1:47496303-47496311 chr1:47496301-47496312
36	FOXA1	chr1:47496729-47497135	T-47D	breast:	n/a	chr1:47496856-47496871
37	NR3C1	chr1:47496653-47497065	A549	lung:	n/a	chr1:47496827-47496853 chr1:47496831-47496849 chr1:47496840-47496847 chr1:47496827-47496853 chr1:47496899-47496925
38	FOXA2	chr1:47496628-47497123	A549	lung:	n/a	n/a
39	FOXA1	chr1:47496702-47497040	A549	lung:	n/a	chr1:47496856-47496871

Variant related genes	Relation type
CYP4X1	TF binding region

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11211424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211425	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211426	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11211436	0.82[JPT][hapmap]
rs11582907	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11584372	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11584400	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588382	0.83[AMR][1000 genomes]
rs11589237	0.81[AMR][1000 genomes]
rs12041262	0.85[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs12141009	0.82[JPT][hapmap]
rs12402481	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12406683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12408055	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12408938	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.91[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12564103	0.83[AMR][1000 genomes]
rs1502909	0.85[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1553390	0.82[JPT][hapmap]
rs17102950	1.00[MEX][hapmap]
rs17102972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17102977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17102978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986925	0.91[ASN][1000 genomes]
rs2036462	0.82[JPT][hapmap]
rs2055498	1.00[MEX][hapmap]
rs2202221	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2202222	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2221324	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2236332	0.81[AMR][1000 genomes]
rs2292059	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2292060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897114	0.91[ASN][1000 genomes]
rs35322032	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3920100	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4531326	0.81[AMR][1000 genomes]
rs55694114	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59244133	0.86[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs61165610	0.80[AMR][1000 genomes]
rs6668901	0.83[AMR][1000 genomes]
rs66753730	0.90[ASN][1000 genomes]
rs74073884	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74073885	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74074332	0.81[AMR][1000 genomes]
rs7549836	0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9699826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9699991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9700422	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9701888	0.89[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs9793989	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[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[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	nsv871958	chr1:47350374-47517123	Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1009338	chr1:47358532-47555253	Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv2763300	chr1:47358532-47628774	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv870695	chr1:47363893-47502714	Bivalent/Poised TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv871288	chr1:47363893-47507808	Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv871377	chr1:47363893-47517123	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv870674	chr1:47416441-47517123	Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv916813	chr1:47435635-47666179	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv871717	chr1:47449486-47524264	Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv461428	chr1:47487585-47524264	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv546167	chr1:47487585-47524264	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv871080	chr1:47489786-47517123	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47490400-47500400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr1:47490600-47498600	Weak transcription	Brain Anterior Caudate	brain
3	chr1:47491000-47501600	Weak transcription	Gastric	stomach
4	chr1:47491600-47517200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr1:47494800-47497600	Enhancers	HUVEC	blood vessel
6	chr1:47495200-47497600	Enhancers	Skeletal Muscle Male	skeletal muscle
7	chr1:47495200-47498600	Enhancers	HMEC	breast
8	chr1:47495200-47499000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:47495600-47497800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:47495800-47497400	Enhancers	Adipose Nuclei	Adipose
11	chr1:47495800-47497600	Enhancers	Aorta	Aorta
12	chr1:47495800-47497600	Enhancers	Stomach Mucosa	stomach
13	chr1:47495800-47497800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:47495800-47498400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr1:47495800-47498600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:47496000-47497800	Enhancers	Pancreas	Pancrea
17	chr1:47496000-47498200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr1:47496000-47501200	Weak transcription	Brain Angular Gyrus	brain
19	chr1:47496400-47497200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:47496400-47497400	Enhancers	Liver	Liver
21	chr1:47496400-47497400	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr1:47496400-47497800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr1:47496600-47497200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:47496600-47497200	Enhancers	Duodenum Mucosa	Duodenum
25	chr1:47496600-47497200	Enhancers	NH-A	brain
26	chr1:47496600-47497400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:47496600-47497400	Enhancers	Right Atrium	heart
28	chr1:47496600-47497400	Flanking Active TSS	NHEK	skin
29	chr1:47496800-47497200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:47496800-47497200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:47496800-47497200	Weak transcription	Esophagus	oesophagus
32	chr1:47496800-47497600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr1:47497000-47497200	Enhancers	Fetal Kidney	kidney
34	chr1:47497000-47497200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr1:47497000-47497600	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr1:47497000-47498800	Enhancers	Hela-S3	cervix

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