Variant report

Variant	rs11125572
Chromosome Location	chr2:55650512-55650513
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	CEBPB	chr2:55650465-55650742	A549	lung:	n/a	chr2:55650607-55650618
2	CEBPB	chr2:55650469-55650768	Hela-S3	cervix:	n/a	chr2:55650607-55650618
3	CEBPB	chr2:55650456-55650787	HepG2	liver:	n/a	chr2:55650607-55650618

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55644949..55647772-chr2:55649501..55651559,3	K562	blood:

Variant related genes	Relation type
CCDC88A	TF binding region
ENSG00000115355	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10169185	0.86[CEU][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10184756	1.00[YRI][hapmap]
rs11125568	0.95[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11125569	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11695152	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12618216	0.87[ASN][1000 genomes]
rs12623954	0.93[ASN][1000 genomes]
rs12713297	0.92[ASN][1000 genomes]
rs1454415	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1454419	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1454420	0.93[ASN][1000 genomes]
rs1454423	0.93[ASN][1000 genomes]
rs1454424	0.93[ASN][1000 genomes]
rs1598163	0.86[CEU][hapmap];0.86[JPT][hapmap]
rs1902061	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1902062	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2045134	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2045135	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2045136	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2123983	0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs2867178	1.00[YRI][hapmap]
rs2867194	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2903509	0.96[YRI][hapmap]
rs2903514	0.91[ASN][1000 genomes]
rs2966466	0.82[CEU][hapmap]
rs3748943	0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs3762511	0.93[ASN][1000 genomes]
rs4277563	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4481025	0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs4672034	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672035	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4672036	0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs4672037	0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs4672038	0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs4672040	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4672041	0.93[ASN][1000 genomes]
rs4672043	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672044	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4672045	0.86[CEU][hapmap];0.80[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6545491	0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs6545492	1.00[CEU][hapmap];0.91[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6705104	0.83[AMR][1000 genomes]
rs6709204	1.00[YRI][hapmap]
rs6720698	1.00[CEU][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6721593	0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs6732633	0.84[ASN][1000 genomes]
rs6732759	0.92[ASN][1000 genomes]
rs6733814	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6744426	0.99[ASN][1000 genomes]
rs6748979	0.93[ASN][1000 genomes]
rs7424286	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7559987	1.00[CEU][hapmap];0.96[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7574743	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7579037	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7589279	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7601340	0.87[CEU][hapmap];0.80[JPT][hapmap]
rs7602189	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7603105	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	nsv1006170	chr2:55530179-55809251	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv520581	chr2:55622825-55903016	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55647800-55652400	Weak transcription	Stomach Mucosa	stomach
2	chr2:55648000-55651000	Weak transcription	HMEC	breast
3	chr2:55648000-55651200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr2:55648000-55651600	Weak transcription	NHEK	skin
5	chr2:55648000-55652200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr2:55648000-55652200	Weak transcription	HUVEC	blood vessel
7	chr2:55648000-55652200	Weak transcription	NH-A	brain
8	chr2:55648000-55652400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:55648000-55652400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:55648000-55652400	Weak transcription	HSMM	muscle
11	chr2:55648000-55653400	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:55648000-55659000	Weak transcription	Adipose Nuclei	Adipose
13	chr2:55648200-55651000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:55648200-55651200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr2:55648200-55652200	Weak transcription	Osteobl	bone
16	chr2:55648400-55651800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:55648400-55652400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr2:55648400-55652400	Enhancers	A549	lung
19	chr2:55648400-55652400	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr2:55648600-55651000	Weak transcription	Brain Cingulate Gyrus	brain
21	chr2:55648600-55651200	Weak transcription	K562	blood
22	chr2:55649200-55651000	Weak transcription	NHLF	lung
23	chr2:55649400-55651400	Weak transcription	NHDF-Ad	bronchial
24	chr2:55649400-55652200	Enhancers	Hela-S3	cervix
25	chr2:55649600-55651200	Enhancers	Brain Hippocampus Middle	brain
26	chr2:55649600-55653000	Enhancers	HepG2	liver
27	chr2:55650000-55651200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:55650000-55652400	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:55650000-55653400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr2:55650000-55659000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:55650200-55650600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:55650200-55651000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:55650200-55652400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr2:55650400-55650800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr2:55650400-55652400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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