Variant report

Variant	rs240339
Chromosome Location	chr22:34048934-34048935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs104860	0.80[EUR][1000 genomes]
rs13055437	0.88[ASN][1000 genomes]
rs19801	0.87[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs240328	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs240330	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs240332	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs240333	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs240335	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs240336	0.83[EUR][1000 genomes]
rs240337	0.89[EUR][1000 genomes]
rs240338	0.96[CEU][hapmap];0.87[CHB][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs240340	0.96[CEU][hapmap];0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs240341	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs240342	0.88[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240343	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]
rs240344	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs240345	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240346	0.88[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240347	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240348	0.96[CEU][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes]
rs240349	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240350	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240351	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240352	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240353	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240355	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240356	0.81[EUR][1000 genomes]
rs240357	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs240358	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs240598	0.89[EUR][1000 genomes]
rs240599	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs240600	0.87[CHB][hapmap];0.89[EUR][1000 genomes]
rs240601	0.87[CHB][hapmap];0.90[EUR][1000 genomes]
rs240602	0.86[EUR][1000 genomes]
rs240603	0.84[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs240604	1.00[CHB][hapmap];0.87[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs240607	0.90[EUR][1000 genomes]
rs240608	0.84[CEU][hapmap]
rs80215	0.87[CHB][hapmap];0.87[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs80231	0.87[CHB][hapmap];0.87[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9621748	0.84[CEU][hapmap];0.87[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 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	nsv1065417	chr22:33823850-34053325	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
8	nsv933309	chr22:33825232-34053000	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
rs240339	CHEK2	cis	parietal	SCAN
rs240339	DEPDC5	cis	cerebellum	SCAN
rs240339	C22orf24	cis	cerebellum	SCAN

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33994200-34050600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr22:33995800-34049800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr22:34003000-34062400	Weak transcription	Gastric	stomach
4	chr22:34007200-34050400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr22:34017000-34050400	Weak transcription	Colonic Mucosa	Colon
6	chr22:34019400-34050600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr22:34021400-34053000	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr22:34033400-34049800	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr22:34036800-34055000	Weak transcription	Brain Anterior Caudate	brain
10	chr22:34037400-34049800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr22:34040200-34056200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr22:34043000-34054800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr22:34043400-34050600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr22:34044400-34062200	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr22:34045200-34049000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr22:34045200-34053000	Weak transcription	Liver	Liver
17	chr22:34045800-34049600	Weak transcription	Psoas Muscle	Psoas
18	chr22:34046200-34049200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr22:34046200-34053400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr22:34046400-34050200	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr22:34046400-34050400	Weak transcription	Fetal Lung	lung
22	chr22:34046400-34053000	Weak transcription	Right Atrium	heart
23	chr22:34046400-34055000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr22:34046400-34055400	Weak transcription	Fetal Muscle Leg	muscle
25	chr22:34046600-34049800	Weak transcription	Lung	lung
26	chr22:34046600-34050200	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr22:34046600-34050600	Weak transcription	Colon Smooth Muscle	Colon
28	chr22:34046600-34052400	Weak transcription	Ovary	ovary
29	chr22:34046600-34053000	Weak transcription	Pancreas	Pancrea
30	chr22:34046600-34056200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr22:34046600-34056400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr22:34046600-34059400	Weak transcription	Primary B cells from peripheral blood	blood
33	chr22:34046800-34049000	Weak transcription	Left Ventricle	heart
34	chr22:34046800-34050200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr22:34046800-34050200	Weak transcription	Aorta	Aorta
36	chr22:34046800-34050600	Weak transcription	Adipose Nuclei	Adipose
37	chr22:34046800-34053000	Weak transcription	Right Ventricle	heart
38	chr22:34046800-34053000	Weak transcription	Stomach Smooth Muscle	stomach
39	chr22:34046800-34053200	Weak transcription	Fetal Stomach	stomach
40	chr22:34046800-34062200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr22:34047000-34049000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr22:34047800-34049800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr22:34048000-34054800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr22:34048200-34049400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr22:34048200-34050600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr22:34048200-34050600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr22:34048400-34049000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr22:34048400-34049200	Enhancers	Fetal Intestine Large	intestine
49	chr22:34048400-34049800	Enhancers	Stomach Mucosa	stomach
50	chr22:34048400-34050400	Enhancers	HepG2	liver

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