Variant report

Variant	rs552122
Chromosome Location	chr11:57525800-57525801
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	EP300	chr11:57525671-57526100	HepG2	liver:	n/a	chr11:57525767-57525781
2	NFIC	chr11:57525596-57526099	HepG2	liver:	n/a	n/a
3	SP1	chr11:57525523-57526061	HepG2	liver:	n/a	n/a
4	FOXA2	chr11:57525568-57526294	HepG2	liver:	n/a	n/a
5	TEAD4	chr11:57525574-57526047	HepG2	liver:	n/a	n/a
6	FOXA1	chr11:57525530-57525960	HepG2	liver:	n/a	n/a
7	FOXA2	chr11:57525614-57525999	HepG2	liver:	n/a	n/a
8	TCF7L2	chr11:57525727-57526050	HepG2	liver:	n/a	chr11:57525861-57525877 chr11:57525865-57525874 chr11:57525865-57525875 chr11:57525862-57525876 chr11:57525861-57525877
9	FOXA1	chr11:57525516-57526173	HepG2	liver:	n/a	n/a
10	FOXA1	chr11:57525570-57526086	HepG2	liver:	n/a	n/a
11	FOXA1	chr11:57525560-57526043	HepG2	liver:	n/a	n/a
12	ARID3A	chr11:57525722-57526028	HepG2	liver:	n/a	n/a
13	EP300	chr11:57525610-57526000	HepG2	liver:	n/a	chr11:57525767-57525781

No.	Distal block	Cell Line	Cell type
1	chr11:57524631..57526806-chr11:57535768..57537369,2	K562	blood:
2	chr11:57525546..57527630-chr11:57527688..57529250,2	K562	blood:
3	chr11:57522258..57527060-chr11:57527676..57532320,5	MCF-7	breast:
4	chr11:57496902..57498702-chr11:57524579..57526641,2	K562	blood:

Variant related genes	Relation type
CTNND1	TF binding region
ENSG00000198561	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10444364	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10736687	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10750868	1.00[CHB][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10896643	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12284427	0.87[AMR][1000 genomes]
rs1313360	1.00[ASN][1000 genomes]
rs1553827	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1798174	1.00[ASN][1000 genomes]
rs1939322	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2860261	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34430954	1.00[ASN][1000 genomes]
rs474073	1.00[CHB][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs474464	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs505995	1.00[ASN][1000 genomes]
rs523739	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs529838	1.00[CHB][hapmap];1.00[YRI][hapmap]
rs542777	1.00[CHB][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs554140	1.00[CHB][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs557051	1.00[CHB][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55786036	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs55838210	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs56879142	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs576786	0.90[AFR][1000 genomes]
rs57759830	1.00[ASN][1000 genomes]
rs58176671	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs585190	1.00[ASN][1000 genomes]
rs58851976	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs59046396	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60076210	1.00[ASN][1000 genomes]
rs60282001	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60897155	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61444907	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61638601	1.00[ASN][1000 genomes]
rs61743110	1.00[ASN][1000 genomes]
rs627861	1.00[ASN][1000 genomes]
rs635663	1.00[CHB][hapmap];0.92[YRI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs637116	0.83[YRI][hapmap];1.00[ASN][1000 genomes]
rs648412	1.00[CHB][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7103407	1.00[CHB][hapmap];0.96[YRI][hapmap];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7103768	1.00[ASN][1000 genomes]
rs7110490	1.00[ASN][1000 genomes]
rs7112557	1.00[ASN][1000 genomes]
rs7118249	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7118308	1.00[ASN][1000 genomes]
rs7122105	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7131175	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73472468	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73474417	1.00[ASN][1000 genomes]
rs73474449	1.00[ASN][1000 genomes]
rs73474453	1.00[ASN][1000 genomes]
rs73474454	1.00[ASN][1000 genomes]
rs73474455	1.00[ASN][1000 genomes]
rs73474476	1.00[ASN][1000 genomes]
rs73482748	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73482786	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73482796	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73482801	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7928666	1.00[ASN][1000 genomes]
rs7938752	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs947940	1.00[CHB][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
4	nsv1040913	chr11:57315006-57696122	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv832164	chr11:57407617-57578825	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv508633	chr11:57419585-57560045	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57510400-57528800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:57511800-57528800	Weak transcription	Fetal Brain Male	brain
3	chr11:57512000-57528800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr11:57512200-57528800	Weak transcription	Colon Smooth Muscle	Colon
5	chr11:57512400-57528800	Weak transcription	HSMM	muscle
6	chr11:57512600-57526400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:57512600-57528800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr11:57512800-57528800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:57513000-57528800	Weak transcription	HSMMtube	muscle
10	chr11:57513200-57528600	Weak transcription	NHEK	skin
11	chr11:57513600-57528800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr11:57513600-57528800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:57513600-57528800	Weak transcription	Colonic Mucosa	Colon
14	chr11:57513600-57529200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:57513600-57531200	Weak transcription	Gastric	stomach
16	chr11:57513800-57528600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr11:57513800-57528600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr11:57513800-57528800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr11:57513800-57528800	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr11:57513800-57528800	Weak transcription	Dnd41	blood
21	chr11:57514000-57528800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr11:57514200-57530000	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr11:57514400-57528600	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr11:57514400-57528800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr11:57514600-57528800	Weak transcription	Placenta	Placenta
26	chr11:57514800-57528600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr11:57514800-57528600	Weak transcription	NH-A	brain
28	chr11:57514800-57528800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:57514800-57528800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr11:57514800-57528800	Weak transcription	Brain Angular Gyrus	brain
31	chr11:57514800-57528800	Weak transcription	Brain Germinal Matrix	brain
32	chr11:57514800-57528800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr11:57514800-57529200	Weak transcription	Lung	lung
34	chr11:57514800-57529200	Weak transcription	Thymus	Thymus
35	chr11:57515000-57528600	Weak transcription	Fetal Muscle Leg	muscle
36	chr11:57515000-57528800	Weak transcription	Stomach Smooth Muscle	stomach
37	chr11:57515200-57528800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr11:57515400-57528600	Weak transcription	Fetal Stomach	stomach
39	chr11:57516000-57528800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr11:57516600-57528800	Weak transcription	Primary B cells from cord blood	blood
41	chr11:57516600-57528800	Weak transcription	Brain Anterior Caudate	brain
42	chr11:57516600-57529200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr11:57516800-57528800	Weak transcription	Fetal Kidney	kidney
44	chr11:57516800-57528800	Weak transcription	Fetal Thymus	thymus
45	chr11:57517200-57528800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr11:57518800-57528600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr11:57518800-57528800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr11:57519600-57528200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:57519800-57528800	Weak transcription	Right Ventricle	heart
50	chr11:57520600-57528800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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