Variant report

Variant	rs9609775
Chromosome Location	chr22:33786251-33786252
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1033373	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1033375	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11089623	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11705582	0.95[ASN][1000 genomes]
rs12484626	0.83[CHB][hapmap];0.82[MEX][hapmap]
rs13347210	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16992213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16992256	0.83[CHB][hapmap]
rs2179057	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2267195	0.92[CHB][hapmap]
rs2267199	0.83[CHB][hapmap];0.83[MEX][hapmap]
rs2283898	0.83[CHB][hapmap]
rs2283899	0.83[CHB][hapmap]
rs2283901	0.83[CHB][hapmap]
rs2283902	0.83[CHB][hapmap]
rs2413181	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.92[MEX][hapmap];0.86[YRI][hapmap];1.00[ASN][1000 genomes]
rs2413182	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[ASN][1000 genomes]
rs5998905	0.85[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[ASN][1000 genomes]
rs5998906	0.96[ASN][1000 genomes]
rs60262384	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60435865	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62225265	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs715487	0.83[CHB][hapmap];0.92[MEX][hapmap]
rs7285067	0.83[CHB][hapmap]
rs7290813	0.83[CHB][hapmap]
rs7291480	0.83[CHB][hapmap]
rs742008	0.83[CHB][hapmap]
rs8142296	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9607037	0.94[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9607038	0.92[CHB][hapmap]
rs9607040	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609772	0.91[CHB][hapmap]
rs9609776	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9609779	0.83[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531587	chr22:33346710-33809338	Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
2	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
3	nsv1067068	chr22:33452180-33851033	Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	32 gene(s)	inside rSNPs	diseases
4	nsv933455	chr22:33532697-33915429	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1059927	chr22:33615699-33904339	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
6	nsv544682	chr22:33615699-33904339	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1061485	chr22:33670971-33885169	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases
8	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
9	nsv1062127	chr22:33755479-34085278	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
10	nsv544683	chr22:33755479-34085278	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
11	esv1835065	chr22:33758698-33798116	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1064026	chr22:33767185-33902059	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA miRNA	2 gene(s)	inside rSNPs	diseases
13	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
14	esv1840336	chr22:33780897-33798116	Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9609775	SEC14L4	cis	cerebellum	SCAN
rs9609775	RHBDD3	cis	parietal	SCAN
rs9609775	TBC1D10A	cis	parietal	SCAN
rs9609775	C22orf24	cis	cerebellum	SCAN
rs9609775	SLC35E4	cis	parietal	SCAN
rs9609775	TIMP3	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:33775000-33789200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr22:33775200-33789000	Weak transcription	Adipose Nuclei	Adipose
3	chr22:33775600-33800400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr22:33776200-33789200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr22:33778000-33790000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr22:33778000-33797200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr22:33778200-33800800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr22:33778600-33798000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr22:33778600-33801000	Weak transcription	GM12878-XiMat	blood
10	chr22:33778600-33852000	Weak transcription	Pancreas	Pancrea
11	chr22:33778800-33786400	Weak transcription	Lung	lung
12	chr22:33778800-33789600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr22:33778800-33796400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr22:33778800-33796800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr22:33778800-33800400	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr22:33779000-33800000	Weak transcription	Fetal Intestine Small	intestine
17	chr22:33779200-33786400	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr22:33780000-33818000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr22:33780200-33802800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr22:33780400-33796600	Weak transcription	Right Ventricle	heart
21	chr22:33780600-33789400	Weak transcription	Ovary	ovary
22	chr22:33780600-33789400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr22:33780600-33796600	Weak transcription	Primary B cells from peripheral blood	blood
24	chr22:33780600-33796800	Weak transcription	Left Ventricle	heart
25	chr22:33780600-33805200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr22:33780600-33834000	Weak transcription	Gastric	stomach
27	chr22:33780800-33789400	Weak transcription	Fetal Intestine Large	intestine
28	chr22:33780800-33823000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr22:33781000-33796600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr22:33781200-33790000	Weak transcription	Duodenum Smooth Muscle	Duodenum
31	chr22:33781200-33793600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr22:33781200-33796200	Weak transcription	Fetal Stomach	stomach
33	chr22:33781200-33814800	Weak transcription	Stomach Smooth Muscle	stomach
34	chr22:33782800-33787200	Weak transcription	HepG2	liver
35	chr22:33785800-33786400	Weak transcription	Fetal Muscle Trunk	muscle
36	chr22:33786000-33786600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr22:33786000-33786600	Enhancers	Brain Germinal Matrix	brain
38	chr22:33786000-33787400	Enhancers	Fetal Lung	lung
39	chr22:33786200-33786400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr22:33786200-33786400	Enhancers	Small Intestine	intestine
41	chr22:33786200-33786600	Enhancers	Fetal Heart	heart
42	chr22:33786200-33786600	Enhancers	NH-A	brain

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