Variant report

Variant	rs2572426
Chromosome Location	chr8:11147123-11147124
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:11146765..11148444-chr8:11152337..11154487,2	K562	blood:
2	chr8:11141173..11146375-chr8:11146983..11151363,11	K562	blood:
3	chr8:11142561..11144389-chr8:11146083..11147788,2	MCF-7	breast:
4	chr8:11141876..11145971-chr8:11146931..11151363,10	K562	blood:

Variant related genes	Relation type
ENSG00000104643	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10091637	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.85[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10108740	0.88[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs11782742	0.96[CEU][hapmap];0.91[GIH][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12680792	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1369368	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1435279	0.85[CEU][hapmap];0.81[CHB][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1529856	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1529858	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1545073	0.96[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2016285	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2060461	0.86[JPT][hapmap]
rs2117616	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2245937	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2256016	0.96[CEU][hapmap];0.89[CHB][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2272594	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2409754	0.96[CEU][hapmap];0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2409755	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2572420	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2572428	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2736258	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[GIH][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2736385	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2736387	0.89[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2736388	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2736390	0.96[CEU][hapmap];0.88[CHB][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3808507	0.96[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3808515	0.96[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.95[GIH][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3808516	0.85[ASN][1000 genomes]
rs3824212	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4410870	0.84[CEU][hapmap]
rs4515509	0.89[EUR][1000 genomes]
rs4841517	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4841518	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4841519	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4841521	0.86[JPT][hapmap]
rs7813424	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035072	chr8:10819444-11480692	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv539473	chr8:10819444-11480692	Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv529399	chr8:10970091-11805960	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
4	nsv831233	chr8:11046854-11234384	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1022525	chr8:11066191-11309356	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv539474	chr8:11066191-11309356	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv1033312	chr8:11126800-11252170	Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2572426	FLJ10661	cis	cerebellum	SCAN
rs2572426	CLDN23	cis	multi-tissue	Pritchard

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:11143000-11149400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:11143000-11162200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr8:11143000-11166400	Weak transcription	Esophagus	oesophagus
4	chr8:11143000-11166400	Weak transcription	Pancreas	Pancrea
5	chr8:11143400-11150200	Weak transcription	Osteobl	bone
6	chr8:11143400-11152800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr8:11143400-11153000	Weak transcription	NHLF	lung
8	chr8:11143400-11153200	Weak transcription	Fetal Thymus	thymus
9	chr8:11143400-11154000	Weak transcription	Psoas Muscle	Psoas
10	chr8:11143400-11163600	Weak transcription	Brain Angular Gyrus	brain
11	chr8:11143400-11166400	Weak transcription	HSMMtube	muscle
12	chr8:11143800-11149200	Weak transcription	K562	blood
13	chr8:11143800-11149400	Weak transcription	Aorta	Aorta
14	chr8:11143800-11153200	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr8:11143800-11169000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr8:11144000-11147800	Weak transcription	Brain Hippocampus Middle	brain
17	chr8:11144000-11152800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr8:11144000-11152800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr8:11144000-11163200	Weak transcription	Right Ventricle	heart
20	chr8:11144200-11152800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr8:11144400-11147200	Strong transcription	HSMM	muscle
22	chr8:11144400-11147600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr8:11144400-11152800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr8:11144400-11153000	Weak transcription	NHEK	skin
25	chr8:11144400-11156000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr8:11144600-11147200	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr8:11144600-11148200	Strong transcription	Primary B cells from cord blood	blood
28	chr8:11144600-11153000	Weak transcription	Fetal Kidney	kidney
29	chr8:11144600-11153400	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr8:11144600-11165200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr8:11144800-11147600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr8:11144800-11148800	Weak transcription	Duodenum Mucosa	Duodenum
33	chr8:11144800-11152800	Weak transcription	Liver	Liver
34	chr8:11144800-11153000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr8:11144800-11153000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr8:11144800-11153200	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr8:11145000-11147200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr8:11145000-11147200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr8:11145000-11147400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr8:11145000-11147400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr8:11145000-11147800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr8:11145000-11147800	Weak transcription	Brain Anterior Caudate	brain
43	chr8:11145000-11149200	Weak transcription	Stomach Mucosa	stomach
44	chr8:11145000-11149800	Weak transcription	Small Intestine	intestine
45	chr8:11145000-11149800	Weak transcription	Hela-S3	cervix
46	chr8:11145000-11149800	Weak transcription	NHDF-Ad	bronchial
47	chr8:11145000-11152600	Weak transcription	Placenta	Placenta
48	chr8:11145000-11152800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr8:11145000-11152800	Weak transcription	Adipose Nuclei	Adipose
50	chr8:11145000-11152800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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