Variant report

Variant	rs2063661
Chromosome Location	chr1:227456849-227456850
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	MYC	chr1:227456780-227456978	MCF10A-Er-Src	breast:	n/a	n/a
2	CEBPB	chr1:227456629-227456992	A549	lung:	n/a	chr1:227456829-227456840
3	EP300	chr1:227456568-227457105	A549	lung:	n/a	n/a
4	POLR2A	chr1:227456739-227456858	MCF10A-Er-Src	breast:	n/a	n/a
5	SP1	chr1:227456609-227457087	A549	lung:	n/a	n/a
6	EP300	chr1:227456664-227457014	A549	lung:	n/a	n/a
7	STAT3	chr1:227456766-227456963	MCF10A-Er-Src	breast:	n/a	n/a
8	TCF7L2	chr1:227456650-227457080	PANC-1	pancreas:	n/a	n/a
9	NR3C1	chr1:227456574-227457049	A549	lung:	n/a	n/a
10	GATA3	chr1:227456659-227457075	A549	lung:	n/a	n/a
11	GATA3	chr1:227456613-227457022	T-47D	breast:	n/a	n/a
12	FOXA1	chr1:227456681-227456970	HepG2	liver:	n/a	chr1:227456853-227456868
13	SP1	chr1:227456549-227457046	A549	lung:	n/a	n/a
14	RFX5	chr1:227456671-227456958	Hela-S3	cervix:	n/a	n/a
15	FOXA2	chr1:227456557-227457187	A549	lung:	n/a	n/a
16	FOS	chr1:227456764-227456908	MCF10A-Er-Src	breast:	n/a	n/a
17	FOXA2	chr1:227456696-227456961	HepG2	liver:	n/a	n/a
18	FOSL2	chr1:227456579-227457039	A549	lung:	n/a	n/a
19	FOS	chr1:227456825-227456855	MCF10A-Er-Src	breast:	n/a	n/a
20	STAT3	chr1:227456788-227456976	MCF10A-Er-Src	breast:	n/a	n/a
21	GATA3	chr1:227456613-227457159	A549	lung:	n/a	n/a
22	FOXA1	chr1:227456626-227457003	T-47D	breast:	n/a	chr1:227456853-227456868
23	NR3C1	chr1:227456623-227456960	A549	lung:	n/a	n/a
24	CEBPB	chr1:227456647-227457170	A549	lung:	n/a	chr1:227456829-227456840
25	FOXA1	chr1:227456662-227456992	HepG2	liver:	n/a	chr1:227456853-227456868
26	REST	chr1:227456610-227457140	A549	lung:	n/a	n/a
27	FOXA1	chr1:227456595-227457036	HepG2	liver:	n/a	chr1:227456853-227456868
28	CEBPB	chr1:227456641-227457050	Hela-S3	cervix:	n/a	chr1:227456829-227456840
29	EP300	chr1:227456724-227456992	Hela-S3	cervix:	n/a	n/a
30	E2F4	chr1:227456787-227457196	MCF10A-Er-Src	breast:	n/a	n/a
31	FOXA1	chr1:227456667-227457004	HepG2	liver:	n/a	chr1:227456853-227456868
32	TCF12	chr1:227456509-227457211	A549	lung:	n/a	n/a
33	POLR2A	chr1:227456639-227457123	PANC-1	pancreas:	n/a	n/a
34	FOXA2	chr1:227456520-227457110	A549	lung:	n/a	n/a
35	CEBPB	chr1:227456674-227457000	A549	lung:	n/a	chr1:227456829-227456840
36	CEBPB	chr1:227456695-227456970	HepG2	liver:	n/a	chr1:227456829-227456840
37	FOXA1	chr1:227456607-227457021	T-47D	breast:	n/a	chr1:227456853-227456868

Variant related genes	Relation type
ENSG00000236636	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10916112	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10916113	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10916116	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10916125	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11576239	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11584325	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11585910	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12119153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12119448	0.84[AFR][1000 genomes]
rs12123597	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12128174	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12131061	0.92[AMR][1000 genomes]
rs12131459	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12131933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12133230	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133633	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12138092	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12138364	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12138383	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12138664	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144205	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12746316	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12747807	0.84[AFR][1000 genomes]
rs12754677	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12755770	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1513607	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1513613	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17613235	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28648445	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34113967	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34702208	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34897490	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35160496	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35952573	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4308948	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs61834323	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61834324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61834326	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61834590	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61834625	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61834626	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660168	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6675572	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6678714	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6697583	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7512871	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7518813	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7523759	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7539662	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7543419	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7548118	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003656	chr1:227034700-227559665	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv535318	chr1:227034700-227559665	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv534002	chr1:227315186-228047108	Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	nsv873242	chr1:227371906-227579344	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv549271	chr1:227411003-227581017	Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:227414000-227459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr1:227431600-227486200	Weak transcription	NHDF-Ad	bronchial
3	chr1:227432000-227459200	Weak transcription	Fetal Lung	lung
4	chr1:227433000-227469000	Weak transcription	Aorta	Aorta
5	chr1:227434600-227468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr1:227434800-227458400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:227435000-227457000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:227443400-227474000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:227445800-227458400	Weak transcription	NHEK	skin
10	chr1:227447200-227473600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr1:227448600-227457200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:227449600-227473600	Weak transcription	NH-A	brain
13	chr1:227449800-227465200	Weak transcription	K562	blood
14	chr1:227452800-227463800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr1:227453000-227468600	Weak transcription	Lung	lung
16	chr1:227453600-227457200	Enhancers	Brain Substantia Nigra	brain
17	chr1:227454200-227470400	Weak transcription	Ovary	ovary
18	chr1:227455000-227457200	Enhancers	Brain Inferior Temporal Lobe	brain
19	chr1:227455200-227457200	Enhancers	Brain Anterior Caudate	brain
20	chr1:227455400-227457000	Enhancers	Brain Angular Gyrus	brain
21	chr1:227455600-227458600	Enhancers	Liver	Liver
22	chr1:227455800-227457000	Enhancers	Adipose Nuclei	Adipose
23	chr1:227456000-227458400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr1:227456000-227458400	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:227456400-227457000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:227456400-227457000	Enhancers	Psoas Muscle	Psoas
27	chr1:227456600-227457000	Enhancers	Small Intestine	intestine
28	chr1:227456600-227457200	Enhancers	HepG2	liver
29	chr1:227456600-227459600	Enhancers	A549	lung
30	chr1:227456600-227468800	Weak transcription	Left Ventricle	heart
31	chr1:227456800-227457000	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr1:227456800-227457000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr1:227456800-227457000	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr1:227456800-227457000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
35	chr1:227456800-227457200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr1:227456800-227457800	Enhancers	HUVEC	blood vessel
37	chr1:227456800-227458000	Enhancers	Pancreatic Islets	Pancreatic Islet

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