Variant report

Variant	rs130407
Chromosome Location	chr22:32472930-32472931
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	22:32053085-32061138..22:32467025-32475239	Hela-S3	cervix:
2	chr22:32413743..32416045-chr22:32472580..32474374,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241878	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs130260	0.84[AMR][1000 genomes]
rs130261	0.84[AMR][1000 genomes]
rs130262	1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs130266	0.85[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs135020	1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs135021	1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs135023	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]
rs135110	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]
rs135111	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413070	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3888536	0.86[CHB][hapmap]
rs4602316	0.86[CHB][hapmap]
rs4821004	0.82[GIH][hapmap];0.90[JPT][hapmap]
rs5753852	1.00[JPT][hapmap];0.84[AMR][1000 genomes]
rs5994466	0.93[ASW][hapmap];0.88[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5994468	0.84[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs5998233	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs5998237	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs5998253	0.86[CHB][hapmap]
rs7291239	0.88[EUR][1000 genomes]
rs8137665	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8139657	0.86[CHB][hapmap]
rs93108	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9606906	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9609433	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[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	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
2	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
3	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
4	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
5	nsv1065175	chr22:32467617-32761093	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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
6	nsv544680	chr22:32467617-32761093	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription 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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs130407	CHEK2	cis	cerebellum	SCAN
rs130407	LARGE	cis	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32460400-32476000	Weak transcription	Pancreas	Pancrea
2	chr22:32468400-32476600	Enhancers	Fetal Intestine Large	intestine
3	chr22:32469400-32489800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr22:32469600-32478200	Genic enhancers	Fetal Intestine Small	intestine
5	chr22:32470800-32473000	Genic enhancers	Duodenum Mucosa	Duodenum
6	chr22:32470800-32474600	Weak transcription	Liver	Liver
7	chr22:32472000-32473000	Enhancers	Right Atrium	heart
8	chr22:32472000-32473400	Enhancers	Colonic Mucosa	Colon
9	chr22:32472000-32473400	Enhancers	Rectal Mucosa Donor 29	rectum
10	chr22:32472200-32473000	Enhancers	Small Intestine	intestine
11	chr22:32472400-32473000	Enhancers	Left Ventricle	heart
12	chr22:32472600-32473000	Enhancers	Fetal Muscle Leg	muscle
13	chr22:32472600-32473000	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr22:32472600-32473000	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr22:32472600-32479200	Weak transcription	Right Ventricle	heart
16	chr22:32472800-32473000	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr22:32472800-32473000	Enhancers	HSMMtube	muscle
18	chr22:32472800-32473200	Enhancers	A549	lung
19	chr22:32472800-32473600	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr22:32472800-32476400	Enhancers	Fetal Heart	heart

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