Variant report

Variant	rs564250
Chromosome Location	chr11:34458861-34458862
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	CBX3	chr11:34458803-34459332	K562	blood:	n/a	n/a
2	RFX5	chr11:34458827-34459019	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:34452352..34457130-chr11:34458043..34461797,6	K562	blood:

Variant related genes	Relation type
CAT	TF binding region
ENSG00000216708	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1014749	0.81[ASN][1000 genomes]
rs1033509	0.91[ASN][1000 genomes]
rs10488737	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs10742316	0.91[ASN][1000 genomes]
rs12421999	0.84[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs16925614	0.93[ASN][1000 genomes]
rs16925668	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs16925678	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs2076556	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs208675	0.98[ASN][1000 genomes]
rs208677	0.98[ASN][1000 genomes]
rs208680	0.99[ASN][1000 genomes]
rs208681	0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs208682	0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs208683	0.87[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2300182	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2746169	0.91[ASN][1000 genomes]
rs3758735	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs3758736	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs4755374	0.97[ASN][1000 genomes]
rs4756146	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4756151	0.82[ASN][1000 genomes]
rs4756155	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs4756156	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs489554	0.98[ASN][1000 genomes]
rs5026711	0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs55665450	0.87[ASN][1000 genomes]
rs7102889	0.93[CHB][hapmap];0.82[CHD][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs7104394	0.87[JPT][hapmap]
rs7106485	0.93[CHB][hapmap];0.88[JPT][hapmap];0.80[ASN][1000 genomes]
rs7109462	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs7109778	0.97[ASN][1000 genomes]
rs7126243	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs7130331	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs7130345	0.87[CHB][hapmap];0.87[JPT][hapmap]
rs72923163	0.87[ASN][1000 genomes]
rs72924903	0.85[ASN][1000 genomes]
rs7395059	0.91[ASN][1000 genomes]
rs7928060	0.82[ASN][1000 genomes]
rs7928866	0.92[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs7938373	0.88[JPT][hapmap]
rs942222	0.87[CHB][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897205	chr11:34248229-34507213	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv897207	chr11:34253683-34621004	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	nsv897208	chr11:34257064-34562247	Strong transcription Weak transcription ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv897209	chr11:34309519-34548906	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
5	nsv832114	chr11:34424428-34607851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv553997	chr11:34458230-34460711	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs564250	CAT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34443800-34460000	Weak transcription	Esophagus	oesophagus
2	chr11:34449400-34459600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr11:34449600-34459200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:34453800-34459000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr11:34453800-34459200	Weak transcription	Adipose Nuclei	Adipose
6	chr11:34454000-34459000	Weak transcription	Primary B cells from cord blood	blood
7	chr11:34454800-34460000	Weak transcription	Lung	lung
8	chr11:34456000-34460000	Weak transcription	Pancreas	Pancrea
9	chr11:34456400-34459800	Weak transcription	HepG2	liver
10	chr11:34457600-34459200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr11:34457800-34459200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr11:34457800-34459400	Weak transcription	NHDF-Ad	bronchial
13	chr11:34457800-34459600	Weak transcription	HSMMtube	muscle
14	chr11:34458000-34459000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr11:34458000-34459000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr11:34458000-34459000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr11:34458000-34459000	Weak transcription	GM12878-XiMat	blood
18	chr11:34458000-34459200	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr11:34458000-34459200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr11:34458000-34459400	Weak transcription	K562	blood
21	chr11:34458200-34459200	Weak transcription	NHEK	skin
22	chr11:34458600-34460200	Flanking Active TSS	Liver	Liver
23	chr11:34458800-34459800	Enhancers	Primary neutrophils fromperipheralblood	blood
24	chr11:34458800-34460000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr11:34458800-34461200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr11:34458800-34463200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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