Variant report

Variant	rs135110
Chromosome Location	chr22:32463875-32463876
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	22:31836635-31847259..22:32461576-32467025	Hela-S3	cervix:
2	22:32053085-32061138..22:32461576-32467025	Hela-S3	cervix:
3	22:32461576-32467025..22:32868055-32872511	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000184708	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000100225	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1056444	0.87[LWK][hapmap];1.00[YRI][hapmap]
rs130260	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs130261	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs130262	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs130266	1.00[ASW][hapmap];0.89[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs130407	0.85[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs135020	1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs135021	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs135023	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];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2246704	0.92[CEU][hapmap];0.81[TSI][hapmap]
rs2413070	0.83[AMR][1000 genomes]
rs2858753	1.00[CEU][hapmap];0.83[TSI][hapmap]
rs3747158	0.84[CEU][hapmap]
rs3888536	0.86[CHB][hapmap]
rs4602316	0.86[CHB][hapmap]
rs4820059	0.81[CEU][hapmap]
rs4821004	1.00[CEU][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.94[LWK][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.82[YRI][hapmap]
rs4821014	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs5753843	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs5753852	0.90[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs5994466	0.92[ASW][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs5994468	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs5998196	0.96[CEU][hapmap];0.80[GIH][hapmap];0.83[TSI][hapmap]
rs5998233	0.92[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs5998237	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5998253	0.86[CHB][hapmap]
rs7291239	0.81[EUR][1000 genomes]
rs739009	0.87[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs8137665	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8139657	0.86[CHB][hapmap]
rs93108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9606906	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9609433	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9609459	0.86[CHB][hapmap]

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	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	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
3	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
4	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
5	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
6	nsv948789	chr22:32462505-32764760	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs135110	CHEK2	cis	cerebellum	SCAN
rs135110	LARGE	cis	cerebellum	SCAN
rs135110	INPP5J	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32442200-32468400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr22:32442200-32469200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr22:32457800-32469400	Weak transcription	Right Ventricle	heart
4	chr22:32460000-32467000	Genic enhancers	Fetal Intestine Small	intestine
5	chr22:32460400-32476000	Weak transcription	Pancreas	Pancrea
6	chr22:32462400-32464200	Enhancers	Left Ventricle	heart
7	chr22:32462400-32468400	Strong transcription	Duodenum Mucosa	Duodenum
8	chr22:32463000-32464000	Strong transcription	Fetal Intestine Large	intestine
9	chr22:32463000-32472000	Weak transcription	Right Atrium	heart
10	chr22:32463200-32464600	Weak transcription	Fetal Heart	heart
11	chr22:32463400-32469400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr22:32463800-32472000	Weak transcription	Colonic Mucosa	Colon

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