Variant report

Variant	rs5762736
Chromosome Location	chr22:29053003-29053004
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:29037415..29040255-chr22:29052758..29055040,2	MCF-7	breast:
2	chr22:29051030..29053991-chr22:29069549..29071319,2	K562	blood:

Variant related genes	Relation type
ENSG00000266503	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10460754	0.93[ASN][1000 genomes]
rs17412920	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17415919	0.82[CEU][hapmap]
rs17504822	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5752766	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5762622	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs5762654	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5762656	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5762659	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5762664	1.00[LWK][hapmap]
rs5762666	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5762686	1.00[ASW][hapmap];0.88[CEU][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];0.88[ASN][1000 genomes]
rs5762758	1.00[ASW][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap]
rs5762763	1.00[ASW][hapmap];1.00[LWK][hapmap];0.80[MEX][hapmap];0.96[MKK][hapmap]
rs5762764	0.80[MEX][hapmap]
rs7286920	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7288416	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73168176	0.91[EUR][1000 genomes]
rs9306455	0.80[EUR][1000 genomes]
rs9306458	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9608692	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9613617	0.81[EUR][1000 genomes]
rs9613630	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9613639	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9613658	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067544	chr22:28755418-29055246	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
2	nsv544674	chr22:28755418-29055246	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS 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 miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv459867	chr22:28993183-29109036	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv588881	chr22:28993183-29109036	Weak transcription Enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1061684	chr22:29026341-29088590	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5762736	CABP7	cis	cerebellum	SCAN
rs5762736	TFIP11	cis	cerebellum	SCAN
rs5762736	TTC28	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29005800-29054000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr22:29017400-29056200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr22:29026600-29053800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr22:29038800-29056400	Weak transcription	Fetal Intestine Small	intestine
5	chr22:29042400-29058200	Weak transcription	Hela-S3	cervix
6	chr22:29046000-29059000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr22:29046400-29073800	Weak transcription	Ovary	ovary
8	chr22:29049000-29059000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr22:29049400-29059200	Weak transcription	Fetal Muscle Leg	muscle
10	chr22:29049600-29053800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr22:29049600-29056600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr22:29050000-29058600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr22:29052000-29053200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr22:29052000-29053400	Enhancers	Fetal Lung	lung
15	chr22:29052200-29053800	Enhancers	Pancreas	Pancrea
16	chr22:29052400-29057200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr22:29052400-29058200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr22:29052600-29055600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr22:29052600-29055800	Weak transcription	Fetal Stomach	stomach
20	chr22:29052600-29074600	Weak transcription	Colon Smooth Muscle	Colon
21	chr22:29053000-29053600	Enhancers	HepG2	liver

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