Variant report

Variant	rs135023
Chromosome Location	chr22:32442776-32442777
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1056444	0.87[LWK][hapmap];1.00[YRI][hapmap]
rs130259	0.83[AFR][1000 genomes]
rs130260	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs130261	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs130262	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs130266	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs130407	0.85[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.87[AMR][1000 genomes]
rs135020	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs135021	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs135110	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs135111	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes]
rs1807550	0.87[EUR][1000 genomes]
rs1986211	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2246704	0.92[CEU][hapmap];0.83[TSI][hapmap]
rs2413070	0.81[AMR][1000 genomes]
rs2858753	1.00[CEU][hapmap];0.86[TSI][hapmap]
rs3747158	0.84[CEU][hapmap]
rs4820059	0.81[CEU][hapmap]
rs4820065	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4821004	1.00[CEU][hapmap];0.82[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.82[YRI][hapmap];0.85[EUR][1000 genomes]
rs4821014	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs5753843	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs5753852	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs5994461	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5994466	0.92[ASW][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs5994468	0.84[AMR][1000 genomes]
rs5998196	0.96[CEU][hapmap];0.86[TSI][hapmap]
rs5998201	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5998204	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5998233	0.92[ASW][hapmap];0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.94[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes]
rs5998237	0.81[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes]
rs739009	0.87[LWK][hapmap];1.00[YRI][hapmap]
rs8137665	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs8142505	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs93108	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9606906	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs9609433	0.84[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055450	chr22:32356150-32468832	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1055925	chr22:32358540-32450200	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv1063876	chr22:32358540-32463271	Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
4	nsv1061546	chr22:32358991-32464350	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
5	nsv1059240	chr22:32362689-32462511	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	nsv544678	chr22:32362689-32462511	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv1060529	chr22:32370432-32525699	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
8	nsv1063267	chr22:32379851-32462650	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv544679	chr22:32379851-32462650	Weak transcription Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
10	nsv1067007	chr22:32400566-32452776	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1065893	chr22:32400566-32453047	Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
12	nsv834177	chr22:32416679-32594663	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
13	esv1803811	chr22:32441022-32509431	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs135023	CHEK2	cis	cerebellum	SCAN
rs135023	INPP5J	cis	cerebellum	SCAN
rs135023	LARGE	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32439200-32444200	Weak transcription	Fetal Heart	heart
2	chr22:32439800-32446000	Weak transcription	Esophagus	oesophagus
3	chr22:32440000-32446400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr22:32440800-32445800	Weak transcription	Stomach Mucosa	stomach
5	chr22:32441200-32455200	Weak transcription	Gastric	stomach
6	chr22:32441600-32444400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr22:32441600-32445600	Weak transcription	Psoas Muscle	Psoas
8	chr22:32441800-32445600	Weak transcription	Fetal Intestine Large	intestine
9	chr22:32441800-32452800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr22:32442000-32445600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr22:32442200-32468400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr22:32442200-32469200	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr22:32442400-32443600	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
14	chr22:32442600-32442800	Enhancers	Small Intestine	intestine
15	chr22:32442600-32443000	Transcr. at gene 5' and 3'	Duodenum Mucosa	Duodenum

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