Variant report

Variant	rs239327
Chromosome Location	chr22:34132955-34132956
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs19964	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs239316	0.83[JPT][hapmap]
rs239321	0.85[CHB][hapmap];0.83[JPT][hapmap]
rs239328	0.84[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs239330	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239331	1.00[ASW][hapmap];1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs239332	0.89[GIH][hapmap]
rs239333	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs239336	0.84[ASW][hapmap];0.92[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.83[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5749654	0.85[CHB][hapmap];0.83[JPT][hapmap]

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	nsv531588	chr22:33776857-34150188	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
3	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
4	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
5	nsv917167	chr22:33852676-34137036	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1062832	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv544686	chr22:33861531-34143295	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
14	nsv1060684	chr22:34108462-34140653	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region lncRNA	2 gene(s)	inside rSNPs	diseases
15	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
16	nsv524432	chr22:34119866-34146368	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs239327	LIMK2	cis	parietal	SCAN
rs239327	CABP7	cis	parietal	SCAN
rs239327	FAM82A1	trans	cerebellum	SCAN
rs239327	PLA2G3	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34105600-34133400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr22:34111200-34146200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr22:34111800-34142800	Weak transcription	Fetal Intestine Small	intestine
4	chr22:34116400-34135800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr22:34120200-34135600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr22:34120400-34135800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr22:34121600-34136800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr22:34123200-34152000	Weak transcription	Aorta	Aorta
9	chr22:34123800-34140800	Weak transcription	Fetal Stomach	stomach
10	chr22:34124800-34133000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr22:34124800-34171000	Weak transcription	Ovary	ovary
12	chr22:34126000-34133000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr22:34126000-34135400	Weak transcription	Right Ventricle	heart
14	chr22:34126000-34137600	Weak transcription	Psoas Muscle	Psoas
15	chr22:34126200-34176200	Weak transcription	Spleen	Spleen
16	chr22:34128200-34133200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr22:34128600-34143200	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr22:34129000-34134400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr22:34129200-34133600	Weak transcription	Left Ventricle	heart
20	chr22:34130200-34133200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr22:34130400-34133800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr22:34130400-34133800	Weak transcription	Fetal Heart	heart
23	chr22:34130600-34133400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr22:34131000-34133200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr22:34131000-34154200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr22:34131200-34133000	Weak transcription	Brain Anterior Caudate	brain
27	chr22:34131200-34133400	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr22:34132000-34133000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr22:34132000-34133600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
30	chr22:34132000-34133800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr22:34132000-34133800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr22:34132600-34133200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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