Variant report

Variant	rs5749646
Chromosome Location	chr22:34097765-34097766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12158758	0.80[MEX][hapmap]
rs2267265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2283930	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5754644	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs5754649	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8135841	0.91[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948523	chr22:33414164-34098417	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	nsv934161	chr22:33979015-34118621	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	nsv1056845	chr22:34066401-34102719	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
12	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
13	nsv519677	chr22:34096135-34098417	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5749646	SEC14L4	cis	parietal	SCAN
rs5749646	SFI1	cis	cerebellum	SCAN
rs5749646	RFPL3	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:34075000-34100400	Weak transcription	Brain Anterior Caudate	brain
2	chr22:34076200-34106400	Weak transcription	Psoas Muscle	Psoas
3	chr22:34081800-34098800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr22:34085600-34103600	Weak transcription	Colon Smooth Muscle	Colon
5	chr22:34087000-34109400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr22:34089800-34099600	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr22:34090400-34100200	Weak transcription	Aorta	Aorta
8	chr22:34090800-34099400	Weak transcription	Esophagus	oesophagus
9	chr22:34091600-34115800	Weak transcription	Pancreas	Pancrea
10	chr22:34092400-34109200	Weak transcription	Fetal Intestine Large	intestine
11	chr22:34093600-34097800	Strong transcription	Primary B cells from peripheral blood	blood
12	chr22:34093800-34098600	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr22:34094000-34099400	Weak transcription	Duodenum Mucosa	Duodenum
14	chr22:34094200-34097800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr22:34094200-34098800	Weak transcription	HepG2	liver
16	chr22:34094400-34102200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr22:34094600-34098200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr22:34095400-34098000	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr22:34095600-34098000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr22:34095600-34098200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr22:34095600-34099200	Weak transcription	Fetal Muscle Leg	muscle
22	chr22:34096200-34097800	Strong transcription	Brain Hippocampus Middle	brain
23	chr22:34096200-34098400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr22:34096400-34097800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr22:34096400-34098400	Strong transcription	Fetal Stomach	stomach
26	chr22:34096400-34103200	Weak transcription	GM12878-XiMat	blood
27	chr22:34096600-34097800	Strong transcription	Skeletal Muscle Male	skeletal muscle
28	chr22:34096800-34098200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
29	chr22:34096800-34098400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr22:34097000-34097800	ZNF genes & repeats	Lung	lung
31	chr22:34097000-34097800	Enhancers	Right Atrium	heart
32	chr22:34097000-34098800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr22:34097000-34099000	Enhancers	Fetal Heart	heart
34	chr22:34097000-34110000	Weak transcription	Ovary	ovary
35	chr22:34097200-34098800	Enhancers	Right Ventricle	heart
36	chr22:34097200-34101200	Weak transcription	Gastric	stomach
37	chr22:34097200-34102200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr22:34097200-34103400	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr22:34097200-34108000	Weak transcription	Fetal Intestine Small	intestine
40	chr22:34097200-34109200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr22:34097200-34109200	Weak transcription	Fetal Brain Female	brain
42	chr22:34097200-34109400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr22:34097400-34098200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr22:34097400-34099000	Enhancers	Left Ventricle	heart
45	chr22:34097400-34103200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr22:34097400-34107400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr22:34097600-34097800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr22:34097600-34098200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr22:34097600-34098200	Enhancers	Spleen	Spleen
50	chr22:34097600-34100400	Weak transcription	Liver	Liver

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