Variant report

Variant	rs57012808
Chromosome Location	chr1:94058716-94058717
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	STAT3	chr1:94058607-94058917	MCF10A-Er-Src	breast:	n/a	chr1:94058751-94058762
2	STAT3	chr1:94058659-94058915	MCF10A-Er-Src	breast:	n/a	chr1:94058751-94058762
3	FOXA1	chr1:94058615-94058819	T-47D	breast:	n/a	n/a
4	POLR2A	chr1:94057236-94058879	HepG2	liver:	n/a	n/a
5	REST	chr1:94058465-94058872	ECC-1	luminal epithelium:	n/a	chr1:94058669-94058682
6	REST	chr1:94058538-94058900	SK-N-SH	brain:	n/a	chr1:94058669-94058682
7	MXI1	chr1:94058292-94059611	IMR90	lung:	n/a	n/a
8	KAP1	chr1:94058613-94058728	U2OS	brain:	n/a	n/a
9	STAT3	chr1:94058607-94058904	MCF10A-Er-Src	breast:	n/a	chr1:94058751-94058762
10	HEY1	chr1:94056860-94058945	HepG2	liver:	n/a	n/a
11	RAD21	chr1:94058548-94058888	SK-N-SH_RA	brain:	n/a	n/a
12	MXI1	chr1:94058049-94059051	SK-N-SH	brain:	n/a	n/a
13	NFIC	chr1:94058426-94059045	ECC-1	luminal epithelium:	n/a	n/a
14	REST	chr1:94058535-94058974	MCF-7	breast:	n/a	chr1:94058669-94058682
15	MYC	chr1:94058589-94058923	MCF10A-Er-Src	breast:	n/a	n/a
16	REST	chr1:94058559-94058837	SK-N-SH	brain:	n/a	chr1:94058669-94058682
17	POLR2A	chr1:94058538-94058867	HepG2	liver:	n/a	n/a
18	EP300	chr1:94058502-94058887	SK-N-SH_RA	brain:	n/a	n/a
19	STAT3	chr1:94058606-94058913	MCF10A-Er-Src	breast:	n/a	chr1:94058751-94058762
20	STAT3	chr1:94058605-94058906	MCF10A-Er-Src	breast:	n/a	chr1:94058751-94058762
21	REST	chr1:94058138-94058936	PFSK-1	brain:	n/a	chr1:94058669-94058682
22	EP300	chr1:94058557-94058893	SK-N-SH_RA	brain:	n/a	n/a
23	NFIC	chr1:94058568-94058891	HepG2	liver:	n/a	n/a
24	POLR2A	chr1:94058583-94058882	Hela-S3	cervix:	n/a	n/a
25	REST	chr1:94058494-94058849	PFSK-1	brain:	n/a	chr1:94058669-94058682
26	REST	chr1:94058471-94058892	ECC-1	luminal epithelium:	n/a	chr1:94058669-94058682
27	MYC	chr1:94058642-94058807	HepG2	liver:	n/a	n/a
28	MAX	chr1:94056964-94059251	HepG2	liver:	n/a	chr1:94057611-94057621
29	FOS	chr1:94058639-94058825	MCF10A-Er-Src	breast:	n/a	n/a
30	POLR2A	chr1:94057268-94058904	HepG2	liver:	n/a	n/a
31	POLR2A	chr1:94057079-94058772	HepG2	liver:	n/a	n/a
32	POLR2A	chr1:94057261-94058811	Hela-S3	cervix:	n/a	n/a
33	REST	chr1:94058586-94058827	PFSK-1	brain:	n/a	chr1:94058669-94058682
34	REST	chr1:94058542-94058885	PFSK-1	brain:	n/a	chr1:94058669-94058682
35	FOS	chr1:94058612-94058902	MCF10A-Er-Src	breast:	n/a	n/a
36	REST	chr1:94058576-94058831	K562	blood:	n/a	chr1:94058669-94058682
37	POLR2A	chr1:94057229-94058804	HepG2	liver:	n/a	n/a
38	MYC	chr1:94058603-94058910	MCF10A-Er-Src	breast:	n/a	n/a
39	POLR2A	chr1:94058360-94058779	Hela-S3	cervix:	n/a	n/a
40	REST	chr1:94058554-94058897	SK-N-SH	brain:	n/a	chr1:94058669-94058682
41	FOS	chr1:94058635-94058835	MCF10A-Er-Src	breast:	n/a	n/a
42	RAD21	chr1:94058680-94058720	HepG2	liver:	n/a	n/a
43	POLR2A	chr1:94057179-94058869	HepG2	liver:	n/a	n/a
44	USF1	chr1:94058631-94058814	SK-N-SH_RA	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000224093	TF binding region
BCAR3	TF binding region

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs12566373	0.82[EUR][1000 genomes]
rs12568405	0.94[EUR][1000 genomes]
rs1618866	0.94[EUR][1000 genomes]
rs17110076	0.88[EUR][1000 genomes]
rs17110124	0.92[ASN][1000 genomes]
rs1740068	0.94[EUR][1000 genomes]
rs182913	0.94[EUR][1000 genomes]
rs183538	0.88[EUR][1000 genomes]
rs2281474	1.00[ASN][1000 genomes]
rs2295330	0.88[EUR][1000 genomes]
rs236266	0.94[EUR][1000 genomes]
rs236274	0.94[EUR][1000 genomes]
rs236275	0.94[EUR][1000 genomes]
rs236278	0.94[EUR][1000 genomes]
rs236281	0.94[EUR][1000 genomes]
rs236322	0.91[ASN][1000 genomes]
rs236323	0.91[ASN][1000 genomes]
rs236326	0.91[ASN][1000 genomes]
rs236329	0.94[ASN][1000 genomes]
rs236330	0.92[ASN][1000 genomes]
rs236331	0.95[ASN][1000 genomes]
rs236332	0.92[ASN][1000 genomes]
rs236333	0.92[ASN][1000 genomes]
rs236335	0.97[ASN][1000 genomes]
rs3754189	0.88[EUR][1000 genomes]
rs3767973	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3767975	0.87[ASN][1000 genomes]
rs3767976	0.92[ASN][1000 genomes]
rs3767977	0.92[ASN][1000 genomes]
rs3767979	0.94[EUR][1000 genomes]
rs3767981	0.94[EUR][1000 genomes]
rs3767987	0.94[EUR][1000 genomes]
rs3767991	0.94[EUR][1000 genomes]
rs57466479	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57914444	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59777284	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60159857	0.94[EUR][1000 genomes]
rs6541380	0.81[EUR][1000 genomes]
rs6661488	0.91[ASN][1000 genomes]
rs6671749	0.95[ASN][1000 genomes]
rs6674143	0.88[EUR][1000 genomes]
rs6692801	0.91[ASN][1000 genomes]
rs6699020	0.81[EUR][1000 genomes]
rs7516400	0.91[ASN][1000 genomes]
rs7518795	0.94[ASN][1000 genomes]
rs7519939	0.95[ASN][1000 genomes]
rs7524368	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7551964	0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482370	chr1:94000799-94183692	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94025600-94073800	Weak transcription	Fetal Brain Female	brain
2	chr1:94041800-94059400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr1:94042200-94063200	Weak transcription	Brain Germinal Matrix	brain
4	chr1:94048200-94059200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr1:94048200-94059400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr1:94048400-94059600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:94048600-94064200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr1:94049600-94059400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr1:94050000-94059400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:94050800-94059200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr1:94053600-94063000	Genic enhancers	Muscle Satellite Cultured Cells	--
12	chr1:94054400-94061000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:94054600-94062000	Weak transcription	Brain Substantia Nigra	brain
14	chr1:94055000-94059200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr1:94055200-94058800	Enhancers	Primary hematopoietic stem cells	blood
16	chr1:94055600-94058800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr1:94055800-94061000	Weak transcription	Aorta	Aorta
18	chr1:94056000-94066000	Weak transcription	Ovary	ovary
19	chr1:94056800-94060200	Enhancers	Pancreas	Pancrea
20	chr1:94057000-94058800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
21	chr1:94057000-94060200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:94057000-94060200	Active TSS	Pancreatic Islets	Pancreatic Islet
23	chr1:94057000-94060200	Genic enhancers	HMEC	breast
24	chr1:94057200-94059000	Flanking Active TSS	Fetal Intestine Large	intestine
25	chr1:94057200-94059000	Enhancers	Fetal Kidney	kidney
26	chr1:94057200-94060000	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr1:94057200-94060200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr1:94057200-94060400	Enhancers	Left Ventricle	heart
29	chr1:94057200-94060400	Enhancers	Psoas Muscle	Psoas
30	chr1:94057400-94059000	Flanking Active TSS	Fetal Intestine Small	intestine
31	chr1:94057400-94068000	Genic enhancers	HSMM	muscle
32	chr1:94057400-94069200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:94057400-94071000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:94057600-94058800	Flanking Active TSS	Colonic Mucosa	Colon
35	chr1:94057600-94058800	Enhancers	Spleen	Spleen
36	chr1:94057600-94059400	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr1:94057600-94061000	Enhancers	Fetal Muscle Trunk	muscle
38	chr1:94057600-94106400	Weak transcription	Primary B cells from cord blood	blood
39	chr1:94057800-94059600	Weak transcription	Osteobl	bone
40	chr1:94057800-94059800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:94057800-94060200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:94057800-94060200	Enhancers	Esophagus	oesophagus
43	chr1:94057800-94061800	Enhancers	Placenta	Placenta
44	chr1:94058000-94059000	Bivalent/Poised TSS	HepG2	liver
45	chr1:94058000-94059200	Active TSS	Rectal Mucosa Donor 29	rectum
46	chr1:94058000-94059600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr1:94058000-94059600	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr1:94058000-94059800	Weak transcription	Fetal Thymus	thymus
49	chr1:94058000-94060000	Bivalent Enhancer	Fetal Heart	heart
50	chr1:94058000-94060000	Enhancers	Stomach Smooth Muscle	stomach

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