Variant report

Variant	rs240343
Chromosome Location	chr22:34053443-34053444
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs104860	0.81[EUR][1000 genomes]
rs13055437	0.88[ASN][1000 genomes]
rs19801	0.87[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs240328	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs240330	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs240332	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs240333	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs240335	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs240336	0.83[EUR][1000 genomes]
rs240337	0.88[EUR][1000 genomes]
rs240338	1.00[CEU][hapmap];0.87[CHB][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs240339	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240340	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs240341	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs240342	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240344	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240345	0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240346	0.83[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240347	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240348	1.00[CEU][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes]
rs240349	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240350	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240352	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240353	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240354	0.95[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240355	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240356	0.82[EUR][1000 genomes]
rs240357	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs240358	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs240598	0.88[EUR][1000 genomes]
rs240599	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs240600	0.87[CHB][hapmap];0.88[EUR][1000 genomes]
rs240601	0.87[CHB][hapmap];0.89[EUR][1000 genomes]
rs240602	0.86[EUR][1000 genomes]
rs240603	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs240604	1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs240607	0.88[EUR][1000 genomes]
rs80215	0.87[CHB][hapmap];0.83[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs80231	0.87[CHB][hapmap];0.82[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9621748	0.88[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1062127	chr22:33755479-34085278	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv544683	chr22:33755479-34085278	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
5	nsv531588	chr22:33776857-34150188	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1055791	chr22:33822226-34159536	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
7	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
8	nsv917167	chr22:33852676-34137036	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv1062832	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv544686	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv914988	chr22:33975998-34083987	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv934161	chr22:33979015-34118621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	nsv588935	chr22:34008430-34073758	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv914989	chr22:34011334-34083987	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs240343	CHEK2	cis	parietal	SCAN
rs240343	C22orf24	cis	cerebellum	SCAN
rs240343	DEPDC5	cis	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34003000-34062400	Weak transcription	Gastric	stomach
2	chr22:34036800-34055000	Weak transcription	Brain Anterior Caudate	brain
3	chr22:34040200-34056200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:34043000-34054800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr22:34044400-34062200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr22:34046400-34055000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr22:34046400-34055400	Weak transcription	Fetal Muscle Leg	muscle
8	chr22:34046600-34056200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr22:34046600-34056400	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr22:34046600-34059400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr22:34046800-34062200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr22:34048000-34054800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr22:34049000-34055000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr22:34050200-34062200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr22:34050400-34053800	Weak transcription	HepG2	liver
16	chr22:34050600-34053600	Weak transcription	Psoas Muscle	Psoas
17	chr22:34050600-34054200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr22:34050800-34057600	Weak transcription	Brain Germinal Matrix	brain
19	chr22:34051000-34055800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr22:34051000-34062200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr22:34051200-34056200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr22:34051600-34054800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr22:34051600-34056200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr22:34052400-34056200	Enhancers	Ovary	ovary
25	chr22:34052400-34063000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr22:34052600-34054200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr22:34052800-34053800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr22:34052800-34053800	Enhancers	Adipose Nuclei	Adipose
29	chr22:34052800-34054000	Enhancers	Colon Smooth Muscle	Colon
30	chr22:34052800-34054200	Enhancers	Fetal Heart	heart
31	chr22:34053000-34053800	Enhancers	Fetal Brain Male	brain
32	chr22:34053000-34053800	Enhancers	Fetal Thymus	thymus
33	chr22:34053000-34053800	Enhancers	Lung	lung
34	chr22:34053000-34053800	Enhancers	Pancreas	Pancrea
35	chr22:34053000-34053800	Enhancers	Rectal Smooth Muscle	rectum
36	chr22:34053000-34053800	Enhancers	Right Atrium	heart
37	chr22:34053000-34053800	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr22:34053000-34054200	Enhancers	Liver	Liver
39	chr22:34053000-34054200	Enhancers	Right Ventricle	heart
40	chr22:34053000-34054200	Enhancers	Stomach Smooth Muscle	stomach
41	chr22:34053000-34056000	Enhancers	Fetal Lung	lung
42	chr22:34053200-34053600	Weak transcription	Left Ventricle	heart
43	chr22:34053200-34053800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr22:34053200-34053800	Enhancers	Fetal Stomach	stomach
45	chr22:34053200-34055000	Weak transcription	NHDF-Ad	bronchial
46	chr22:34053200-34056400	Weak transcription	Stomach Mucosa	stomach
47	chr22:34053400-34053600	Enhancers	Brain Hippocampus Middle	brain
48	chr22:34053400-34054000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr22:34053400-34062200	Weak transcription	Fetal Brain Female	brain

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