Variant report

Variant	rs239336
Chromosome Location	chr22:34141321-34141322
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs19964	0.90[CHB][hapmap]
rs239321	0.85[CHB][hapmap]
rs239327	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]
rs239328	1.00[ASW][hapmap];0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs239330	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];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs239331	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]
rs239333	0.92[CEU][hapmap];0.91[CHB][hapmap];0.83[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs5749654	0.85[CHB][hapmap]

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	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	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
14	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
15	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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs239336	CABP7	cis	parietal	SCAN
rs239336	PLA2G3	cis	parietal	SCAN
rs239336	LIMK2	cis	parietal	SCAN
rs239336	GAL3ST1	cis	cerebellum	SCAN

Chromatin state (count:47 , 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	chr22:34124800-34171000	Weak transcription	Ovary	ovary
5	chr22:34126200-34176200	Weak transcription	Spleen	Spleen
6	chr22:34128600-34143200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr22:34131000-34154200	Weak transcription	Brain Cingulate Gyrus	brain
8	chr22:34133800-34147600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr22:34134400-34164800	Weak transcription	Brain Anterior Caudate	brain
10	chr22:34136200-34148600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:34136200-34152800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr22:34136200-34152800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr22:34136400-34152600	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr22:34136800-34141400	Weak transcription	Right Atrium	heart
15	chr22:34136800-34152600	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr22:34137200-34144400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr22:34137200-34151000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr22:34137400-34152600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr22:34137600-34151000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr22:34137800-34152800	Weak transcription	Colon Smooth Muscle	Colon
21	chr22:34138000-34144400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr22:34138000-34148600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr22:34138000-34152600	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr22:34138000-34152800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr22:34138000-34160800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr22:34138600-34141400	Weak transcription	Fetal Muscle Leg	muscle
27	chr22:34138600-34141400	Weak transcription	Psoas Muscle	Psoas
28	chr22:34139400-34141600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr22:34139800-34142600	Weak transcription	HepG2	liver
30	chr22:34140200-34142400	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr22:34140400-34141800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr22:34140400-34141800	Enhancers	Left Ventricle	heart
33	chr22:34140400-34141800	Enhancers	Lung	lung
34	chr22:34140400-34142200	Enhancers	Gastric	stomach
35	chr22:34140600-34141400	Weak transcription	Right Ventricle	heart
36	chr22:34140800-34141600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr22:34140800-34142200	Enhancers	Fetal Lung	lung
38	chr22:34140800-34146000	Enhancers	Fetal Heart	heart
39	chr22:34140800-34149200	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr22:34140800-34152600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr22:34141000-34141600	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr22:34141000-34141600	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr22:34141000-34144400	Weak transcription	GM12878-XiMat	blood
44	chr22:34141000-34145000	Enhancers	Stomach Mucosa	stomach
45	chr22:34141200-34141800	Genic enhancers	Fetal Stomach	stomach
46	chr22:34141200-34142000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr22:34141200-34144400	Weak transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links