Variant report

Variant	rs57267169
Chromosome Location	chr2:58396442-58396443
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	chr2:58396129-58396455	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:58273167..58274943-chr2:58395167..58397109,2	K562	blood:

Variant related genes	Relation type
FANCL	TF binding region
ENSG00000028116	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10184957	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11900900	0.81[AFR][1000 genomes]
rs11903212	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12616896	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12624152	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12713376	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12988249	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13006005	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13023405	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13032851	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13410228	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13422760	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1404457	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1404459	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1404460	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34335951	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34556232	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35773188	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35925771	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755296	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3771222	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55809167	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61746304	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6709533	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6714952	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6752935	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7558066	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7561771	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9309303	0.95[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv458052	chr2:58388696-58450569	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv582098	chr2:58388696-58450569	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv817995	chr2:58390538-58450569	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58349000-58421200	Weak transcription	Brain Substantia Nigra	brain
2	chr2:58359000-58399000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
4	chr2:58359200-58399200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr2:58363400-58399000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr2:58363600-58406800	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:58365600-58438000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:58368200-58403000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:58368200-58417000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:58368600-58399000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:58374400-58397400	Weak transcription	Fetal Heart	heart
12	chr2:58380800-58398800	Weak transcription	Spleen	Spleen
13	chr2:58381000-58398800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:58382600-58400200	Weak transcription	Brain Germinal Matrix	brain
15	chr2:58382600-58400400	Weak transcription	Gastric	stomach
16	chr2:58382800-58398800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr2:58382800-58398800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:58382800-58399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:58383000-58415600	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:58383200-58398800	Weak transcription	Esophagus	oesophagus
21	chr2:58383200-58415000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:58385000-58421200	Weak transcription	Left Ventricle	heart
23	chr2:58385200-58398200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr2:58385200-58424600	Weak transcription	Ovary	ovary
25	chr2:58385400-58400400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr2:58387800-58396600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:58388400-58398200	Weak transcription	Fetal Muscle Trunk	muscle
28	chr2:58388600-58397400	Weak transcription	Brain Anterior Caudate	brain
29	chr2:58388800-58397600	Weak transcription	Fetal Brain Female	brain
30	chr2:58388800-58401800	Weak transcription	Primary B cells from peripheral blood	blood
31	chr2:58388800-58437400	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:58389000-58398000	Weak transcription	HSMM	muscle
33	chr2:58389000-58423200	Weak transcription	NHLF	lung
34	chr2:58389200-58397600	Weak transcription	Primary hematopoietic stem cells	blood
35	chr2:58389400-58397000	Weak transcription	Primary B cells from cord blood	blood
36	chr2:58389600-58431000	Weak transcription	HUVEC	blood vessel
37	chr2:58389800-58397400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr2:58389800-58421000	Weak transcription	K562	blood
39	chr2:58390000-58397400	Weak transcription	Adipose Nuclei	Adipose
40	chr2:58390000-58399000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:58390200-58421200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr2:58390400-58400800	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr2:58390600-58397400	Weak transcription	HepG2	liver
44	chr2:58390600-58398800	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr2:58391000-58467000	Weak transcription	HMEC	breast
46	chr2:58392200-58398800	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr2:58392200-58414200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr2:58392600-58408200	Weak transcription	A549	lung
49	chr2:58392600-58415600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr2:58393000-58397400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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