Variant report

Variant	rs557812
Chromosome Location	chr1:93507888-93507889
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93507541..93509653-chr1:93511685..93513516,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11164860	0.86[ASN][1000 genomes]
rs11164861	0.84[ASN][1000 genomes]
rs12022729	0.95[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs12023767	0.85[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs12027025	0.94[ASN][1000 genomes]
rs12039256	0.94[ASN][1000 genomes]
rs12043577	0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs12119421	0.93[ASN][1000 genomes]
rs12130551	0.84[ASN][1000 genomes]
rs12134501	0.94[ASN][1000 genomes]
rs12141895	0.94[ASN][1000 genomes]
rs1678778	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2086312	0.85[ASN][1000 genomes]
rs2253595	0.95[ASN][1000 genomes]
rs2492898	0.93[ASN][1000 genomes]
rs2815417	0.84[JPT][hapmap]
rs2928183	0.86[ASN][1000 genomes]
rs4626900	0.93[ASN][1000 genomes]
rs4847227	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs485336	0.94[ASN][1000 genomes]
rs486370	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs492054	0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.86[ASN][1000 genomes]
rs492754	0.86[CHB][hapmap];0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs496465	0.87[CHB][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];0.86[ASN][1000 genomes]
rs497540	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs504418	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs517856	0.92[ASN][1000 genomes]
rs521527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs524045	0.93[ASN][1000 genomes]
rs544285	0.84[JPT][hapmap]
rs553396	0.87[ASN][1000 genomes]
rs56320266	0.84[ASN][1000 genomes]
rs572131	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs57478994	0.93[ASN][1000 genomes]
rs590296	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs591820	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs591868	0.87[ASN][1000 genomes]
rs592751	0.90[CHB][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs664524	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs664852	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6674738	0.84[ASN][1000 genomes]
rs680285	0.95[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs808833	0.95[CHB][hapmap];0.92[CHD][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs9787147	1.00[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv870775	chr1:93481640-93543119	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs557812	MTF2	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93507400-93508600	Flanking Active TSS	Dnd41	blood
2	chr1:93507400-93508600	Flanking Active TSS	GM12878-XiMat	blood
3	chr1:93507600-93508000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
4	chr1:93507600-93508000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
5	chr1:93507600-93508000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
6	chr1:93507600-93508000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
7	chr1:93507600-93508000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:93507600-93508000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:93507600-93508000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
10	chr1:93507600-93508000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
11	chr1:93507600-93508000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
12	chr1:93507600-93508200	Enhancers	Fetal Intestine Small	intestine
13	chr1:93507600-93508400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr1:93507600-93508400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:93507600-93508600	Flanking Active TSS	Primary B cells from peripheral blood	blood
16	chr1:93507600-93508600	Flanking Active TSS	Primary T cells from cord blood	blood
17	chr1:93507600-93508600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr1:93507600-93508600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr1:93507600-93508600	Active TSS	Colonic Mucosa	Colon
20	chr1:93507600-93508600	Active TSS	Fetal Intestine Large	intestine
21	chr1:93507600-93508800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr1:93507600-93508800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:93507600-93508800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr1:93507600-93508800	Flanking Active TSS	Liver	Liver
25	chr1:93507600-93508800	Active TSS	Duodenum Mucosa	Duodenum
26	chr1:93507800-93508000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr1:93507800-93508000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr1:93507800-93508000	Flanking Active TSS	Fetal Thymus	thymus
29	chr1:93507800-93508000	Flanking Active TSS	Sigmoid Colon	Sigmoid Colon
30	chr1:93507800-93508000	Flanking Active TSS	K562	blood
31	chr1:93507800-93508200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:93507800-93508200	Enhancers	Primary B cells from cord blood	blood
33	chr1:93507800-93508200	Active TSS	HepG2	liver
34	chr1:93507800-93508400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr1:93507800-93508400	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr1:93507800-93508400	Flanking Active TSS	Thymus	Thymus
37	chr1:93507800-93508400	Enhancers	A549	lung
38	chr1:93507800-93508600	Enhancers	Stomach Mucosa	stomach
39	chr1:93507800-93508600	Active TSS	Monocytes-CD14+_RO01746	blood

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