Variant report

Variant	rs133940
Chromosome Location	chr22:33397425-33397426
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:33386658..33389072-chr22:33395353..33398273,2	MCF-7	breast:
2	22:32920308-32927723..22:33389304-33403028	K562	blood:

Variant related genes	Relation type
ENSG00000185666	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs133953	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs133955	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs133968	1.00[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs241710	0.89[CHB][hapmap]
rs241713	0.89[CHB][hapmap]
rs241716	0.89[CHB][hapmap]
rs241720	0.87[CHB][hapmap]
rs241723	0.88[CHB][hapmap]
rs241726	0.84[ASW][hapmap];0.90[GIH][hapmap]
rs241734	0.89[CHB][hapmap]
rs470009	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs470012	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531568	chr22:33336868-33480272	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv531587	chr22:33346710-33809338	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs133940	SYN3	cis	parietal	SCAN
rs133940	TIMP3	cis	cerebellum	SCAN
rs133940	SYN3	cis	cerebellum	SCAN
rs133940	C22orf27	cis	cerebellum	SCAN
rs133940	XBP1	cis	cerebellum	SCAN
rs133940	C22orf27	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33382400-33404200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr22:33388200-33400000	Weak transcription	Brain Angular Gyrus	brain
3	chr22:33388400-33401000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr22:33390800-33399800	Weak transcription	Fetal Brain Female	brain
5	chr22:33391600-33399800	Weak transcription	HepG2	liver
6	chr22:33391800-33398400	Enhancers	HMEC	breast
7	chr22:33393000-33398400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr22:33393400-33399800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr22:33395000-33398200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr22:33395000-33398800	Enhancers	NHEK	skin
11	chr22:33395000-33399000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr22:33396200-33397600	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr22:33396400-33398400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr22:33396600-33397600	Weak transcription	Hela-S3	cervix
15	chr22:33396600-33399800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr22:33396800-33397600	Genic enhancers	HUES48 Cell Line	embryonic stem cell
17	chr22:33396800-33399800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr22:33396800-33399800	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr22:33396800-33399800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr22:33396800-33401800	Weak transcription	Brain Hippocampus Middle	brain
21	chr22:33397000-33399800	Weak transcription	Brain Germinal Matrix	brain
22	chr22:33397200-33397600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr22:33397200-33397800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr22:33397200-33398800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr22:33397200-33399800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr22:33397200-33400600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr22:33397400-33398000	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr22:33397400-33398800	Weak transcription	HUES64 Cell Line	embryonic stem cell

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