Variant report

Variant	rs4654058
Chromosome Location	chr1:224806174-224806175
allele	C/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	ZNF263	chr1:224805924-224806496	HEK293-T-REx	kidney:	n/a	chr1:224806279-224806288
2	SUZ12	chr1:224803428-224806408	NT2-D1	testis:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:224805248..224807412-chr1:224827891..224830752,2	K562	blood:

Variant related genes	Relation type
ENSG00000233384	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10916653	0.81[EUR][1000 genomes]
rs12564263	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1353837	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1566386	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs1566387	0.85[CEU][hapmap]
rs1566388	0.84[EUR][1000 genomes]
rs16850250	0.81[CHD][hapmap]
rs1932991	0.80[EUR][1000 genomes]
rs2405317	0.83[EUR][1000 genomes]
rs4654057	0.84[EUR][1000 genomes]
rs4654060	0.80[EUR][1000 genomes]
rs6658957	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6665204	0.83[EUR][1000 genomes]
rs6690184	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6697510	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs6699331	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7516323	0.81[EUR][1000 genomes]
rs7529774	0.84[EUR][1000 genomes]
rs7532595	0.83[EUR][1000 genomes]
rs883115	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[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs904505	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014717	chr1:224551939-224885543	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv535311	chr1:224551939-224885543	Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4654058	C1orf58	cis	parietal	SCAN
rs4654058	SNRK	trans	parietal	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:224803200-224806400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr1:224803200-224806400	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
3	chr1:224803200-224807000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
4	chr1:224803200-224807000	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:224803200-224807200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:224803200-224807400	Active TSS	NHDF-Ad	bronchial
7	chr1:224803400-224806800	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
8	chr1:224803600-224806200	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
9	chr1:224803600-224806400	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:224803800-224806200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr1:224803800-224806200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr1:224803800-224807800	Active TSS	NH-A	brain
13	chr1:224804200-224806200	Bivalent/Poised TSS	Fetal Kidney	kidney
14	chr1:224804400-224806400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:224804600-224806600	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
16	chr1:224804800-224806200	Bivalent Enhancer	Fetal Thymus	thymus
17	chr1:224804800-224807000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
18	chr1:224805000-224806200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
19	chr1:224805000-224806400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:224805000-224806400	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:224805000-224806600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
22	chr1:224805000-224807000	Bivalent/Poised TSS	Osteobl	bone
23	chr1:224805200-224806200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:224805200-224806200	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:224805200-224806400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
26	chr1:224805200-224806400	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:224805400-224806200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr1:224805400-224806400	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
29	chr1:224805400-224807400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr1:224805400-224808000	Flanking Active TSS	Dnd41	blood
31	chr1:224805600-224806200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
32	chr1:224805600-224806200	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
33	chr1:224805600-224806800	Bivalent Enhancer	Primary T cells from cord blood	blood
34	chr1:224805600-224807200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr1:224805800-224806200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
36	chr1:224805800-224806200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr1:224805800-224806200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
38	chr1:224805800-224806200	Active TSS	Pancreas	Pancrea
39	chr1:224805800-224806200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
40	chr1:224805800-224806400	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
41	chr1:224805800-224806400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:224805800-224806400	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr1:224805800-224806400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr1:224805800-224806800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
45	chr1:224805800-224812200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr1:224806000-224806200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
47	chr1:224806000-224806200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:224806000-224806200	Active TSS	HMEC	breast
49	chr1:224806000-224806200	Bivalent/Poised TSS	NHLF	lung
50	chr1:224806000-224806400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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