Variant report

Variant	rs2227023
Chromosome Location	chr22:34213356-34213357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1018786	0.81[GIH][hapmap]
rs110689	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs13057617	1.00[CHD][hapmap]
rs1573654	0.81[GIH][hapmap]
rs173237	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs2018743	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs238857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs238862	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs238863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.81[EUR][1000 genomes]
rs2413201	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs28374	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap]
rs2899213	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs379239	0.89[ASN][1000 genomes]
rs419898	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs424576	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs424784	1.00[CHB][hapmap];0.82[JPT][hapmap]
rs444993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs447336	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs454398	0.89[ASN][1000 genomes]
rs481698	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs4820118	1.00[CHB][hapmap]
rs4821186	0.87[LWK][hapmap]
rs4821187	1.00[CHB][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493192	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes]
rs496956	1.00[CHB][hapmap]
rs5749665	1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.86[TSI][hapmap];1.00[ASN][1000 genomes]
rs5749668	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs5749674	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs5754676	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs5754679	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs5754682	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs5754698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754707	0.81[ASN][1000 genomes]
rs722659	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs738942	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs867124	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv934109	chr22:33722066-34339500	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
2	esv2763261	chr22:33831348-34288389	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1057450	chr22:33928913-34849012	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv914990	chr22:34090440-34373293	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv914991	chr22:34106384-34293516	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv459878	chr22:34106745-34226592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv588936	chr22:34106745-34226592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1056553	chr22:34116979-34286191	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv914992	chr22:34135007-34283144	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv524156	chr22:34145596-34260738	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv1064781	chr22:34152145-34231792	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv529886	chr22:34153740-34258847	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv1061736	chr22:34178034-34394918	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
14	nsv544689	chr22:34178034-34394918	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	nsv526550	chr22:34204930-34221959	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv1056001	chr22:34206144-34221959	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2227023	SMTN	cis	cerebellum	SCAN
rs2227023	KREMEN1	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34200600-34234200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr22:34207600-34215600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr22:34208200-34219600	Weak transcription	Aorta	Aorta
4	chr22:34208400-34214600	Weak transcription	Ovary	ovary
5	chr22:34208400-34217200	Weak transcription	Fetal Lung	lung
6	chr22:34208600-34214400	Weak transcription	GM12878-XiMat	blood
7	chr22:34208600-34217200	Weak transcription	Colon Smooth Muscle	Colon
8	chr22:34208600-34217200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr22:34208600-34217400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr22:34208800-34215800	Weak transcription	Psoas Muscle	Psoas
11	chr22:34208800-34215800	Weak transcription	Right Atrium	heart
12	chr22:34208800-34217200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr22:34208800-34217600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr22:34208800-34219600	Weak transcription	Pancreas	Pancrea
15	chr22:34209000-34213800	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr22:34209000-34216000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr22:34209000-34217200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr22:34209200-34213400	Weak transcription	Left Ventricle	heart
19	chr22:34209200-34214800	Weak transcription	Right Ventricle	heart
20	chr22:34209200-34216800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr22:34209400-34217200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr22:34209800-34213400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr22:34210000-34213600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr22:34212000-34213800	Weak transcription	Fetal Heart	heart
25	chr22:34212000-34214000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr22:34212000-34217000	Weak transcription	Stomach Smooth Muscle	stomach
27	chr22:34212600-34213400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr22:34212600-34213600	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr22:34212600-34221600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr22:34212800-34213400	Enhancers	Fetal Brain Male	brain
31	chr22:34213000-34228000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr22:34213200-34214600	Weak transcription	Fetal Stomach	stomach
33	chr22:34213200-34216800	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr22:34213200-34232200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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