Variant report

Variant	rs2267282
Chromosome Location	chr22:34159536-34159537
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11089631	0.88[CHB][hapmap];0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs11703278	0.83[CHB][hapmap];0.84[ASN][1000 genomes]
rs11705248	0.83[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs12167740	0.84[ASN][1000 genomes]
rs12169879	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12170014	0.81[ASN][1000 genomes]
rs12628434	0.84[ASN][1000 genomes]
rs13053313	0.83[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.83[ASN][1000 genomes]
rs16993099	1.00[YRI][hapmap]
rs17735172	1.00[YRI][hapmap]
rs189444	0.82[ASN][1000 genomes]
rs2157088	1.00[YRI][hapmap]
rs2267285	0.91[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2267286	0.91[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2267288	0.89[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2267293	0.83[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs2267294	0.83[CHB][hapmap];0.81[CHD][hapmap];0.80[JPT][hapmap]
rs2283939	0.91[CEU][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2283943	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2283944	0.98[ASN][1000 genomes]
rs2283945	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283946	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283949	0.83[CHB][hapmap];0.80[JPT][hapmap];0.84[ASN][1000 genomes]
rs4820111	0.91[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4820112	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4820113	0.83[CHB][hapmap];0.80[JPT][hapmap];0.82[ASN][1000 genomes]
rs4821182	0.82[GIH][hapmap]
rs4821184	1.00[YRI][hapmap]
rs4821185	1.00[YRI][hapmap]
rs491508	0.82[CHD][hapmap]
rs496210	0.81[JPT][hapmap]
rs5999095	0.91[CEU][hapmap];0.89[CHB][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs715482	0.88[CHB][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7286415	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7286428	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73170589	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs743704	0.94[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs743705	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8138783	0.87[EUR][1000 genomes]
rs8138903	1.00[YRI][hapmap]
rs9619374	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv1055791	chr22:33822226-34159536	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv1055203	chr22:34098417-34196685	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv529885	chr22:34150132-34182300	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	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
15	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2267282	LIMK2	cis	parietal	SCAN
rs2267282	PLA2G3	cis	parietal	SCAN
rs2267282	RNF215	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34124800-34171000	Weak transcription	Ovary	ovary
2	chr22:34126200-34176200	Weak transcription	Spleen	Spleen
3	chr22:34134400-34164800	Weak transcription	Brain Anterior Caudate	brain
4	chr22:34138000-34160800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr22:34143400-34160000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr22:34147400-34168600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr22:34149200-34167000	Weak transcription	Brain Angular Gyrus	brain
8	chr22:34151800-34167000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr22:34153200-34164800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr22:34153400-34169000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr22:34153600-34160200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr22:34154200-34169600	Weak transcription	Psoas Muscle	Psoas
13	chr22:34154400-34160600	Weak transcription	Fetal Muscle Leg	muscle
14	chr22:34154400-34165200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr22:34154400-34166400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr22:34154400-34167200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr22:34154400-34171000	Weak transcription	Colon Smooth Muscle	Colon
18	chr22:34154400-34175800	Weak transcription	Fetal Stomach	stomach
19	chr22:34154400-34176000	Weak transcription	Gastric	stomach
20	chr22:34154600-34162000	Weak transcription	Right Ventricle	heart
21	chr22:34154800-34162000	Weak transcription	Left Ventricle	heart
22	chr22:34154800-34164600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr22:34154800-34164600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr22:34154800-34164600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr22:34154800-34167200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr22:34155000-34164600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr22:34155000-34164600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr22:34155000-34164800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr22:34155000-34164800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr22:34155200-34164400	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr22:34156600-34164800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr22:34157800-34159600	Weak transcription	Primary B cells from peripheral blood	blood
33	chr22:34158800-34159800	Enhancers	Fetal Heart	heart
34	chr22:34159400-34159800	Enhancers	GM12878-XiMat	blood

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