Variant report

Variant	rs239332
Chromosome Location	chr22:34137267-34137268
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr22:34136929-34137288	H1-neurons	neurons:	n/a	n/a
2	POLR2A	chr22:34136554-34137851	K562	blood:	n/a	n/a
3	POLR2A	chr22:34136942-34137289	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
LARGE-AS1	TF binding region

Extended variants
information (count: 22 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs239327	0.89[GIH][hapmap]
rs239328	0.89[GIH][hapmap]
rs239330	0.89[GIH][hapmap]
rs239331	0.89[GIH][hapmap]
rs45774	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4821181	0.94[CHB][hapmap];0.85[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	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	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs239332	CCDC157	cis	parietal	SCAN
rs239332	AP1B1	cis	cerebellum	SCAN
rs239332	LIMK2	cis	parietal	SCAN
rs239332	LIMK2	cis	cerebellum	SCAN
rs239332	BPIL2	cis	parietal	SCAN
rs239332	PLA2G3	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34111200-34146200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr22:34111800-34142800	Weak transcription	Fetal Intestine Small	intestine
3	chr22:34123200-34152000	Weak transcription	Aorta	Aorta
4	chr22:34123800-34140800	Weak transcription	Fetal Stomach	stomach
5	chr22:34124800-34171000	Weak transcription	Ovary	ovary
6	chr22:34126000-34137600	Weak transcription	Psoas Muscle	Psoas
7	chr22:34126200-34176200	Weak transcription	Spleen	Spleen
8	chr22:34128600-34143200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr22:34131000-34154200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr22:34133000-34138000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr22:34133200-34137600	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr22:34133600-34140400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr22:34133800-34138000	Enhancers	Fetal Heart	heart
14	chr22:34133800-34147600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr22:34134000-34140400	Weak transcription	Lung	lung
16	chr22:34134400-34164800	Weak transcription	Brain Anterior Caudate	brain
17	chr22:34134600-34138000	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr22:34134800-34138000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr22:34135000-34139200	Enhancers	Left Ventricle	heart
20	chr22:34135600-34141000	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr22:34135800-34137600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr22:34136000-34140200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr22:34136200-34137400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr22:34136200-34137600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr22:34136200-34140600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr22:34136200-34148600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr22:34136200-34152800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr22:34136200-34152800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr22:34136400-34152600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr22:34136800-34138800	Enhancers	Primary B cells from peripheral blood	blood
31	chr22:34136800-34141400	Weak transcription	Right Atrium	heart
32	chr22:34136800-34152600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr22:34137000-34137400	Weak transcription	Right Ventricle	heart
34	chr22:34137000-34137600	Enhancers	GM12878-XiMat	blood
35	chr22:34137000-34137800	Enhancers	Colon Smooth Muscle	Colon
36	chr22:34137200-34137400	Enhancers	Rectal Smooth Muscle	rectum
37	chr22:34137200-34138000	Enhancers	Stomach Smooth Muscle	stomach
38	chr22:34137200-34140200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr22:34137200-34144400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr22:34137200-34151000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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