Variant report

Variant	rs4822983
Chromosome Location	chr22:29115066-29115067
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1033667	0.90[CEU][hapmap]
rs12628239	0.86[EUR][1000 genomes]
rs1547014	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[YRI][hapmap];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1807609	0.82[AFR][1000 genomes]
rs2078555	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4352308	0.83[AFR][1000 genomes]
rs4820791	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs5752773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752774	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752775	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5752776	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5762760	0.83[CEU][hapmap]
rs6005840	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs738722	0.90[CEU][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs9613667	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916473	chr22:28837041-29215603	Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv9895	chr22:29029961-29184277	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1064624	chr22:29065528-29130728	Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1064079	chr22:29065528-29456059	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	nsv513775	chr22:29083731-29137822	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv834169	chr22:29095446-29303929	Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
7	nsv517951	chr22:29105558-29135889	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Esophageal cancer (squamous cell)	22960999	GWAS catalog

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:29076200-29137600	Weak transcription	Esophagus	oesophagus
2	chr22:29076400-29119200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr22:29076400-29129400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr22:29079600-29130200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr22:29082800-29137600	Weak transcription	Spleen	Spleen
6	chr22:29083000-29126600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr22:29085000-29116600	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr22:29088600-29118600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr22:29090200-29129000	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr22:29090600-29137200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr22:29090600-29137200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr22:29091000-29116600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr22:29091000-29120200	Weak transcription	Placenta	Placenta
14	chr22:29093600-29121800	Weak transcription	Small Intestine	intestine
15	chr22:29093600-29132000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
16	chr22:29093800-29126600	Weak transcription	Gastric	stomach
17	chr22:29094600-29125000	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr22:29097000-29130800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr22:29099800-29129000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr22:29100400-29137200	Weak transcription	Pancreas	Pancrea
21	chr22:29101200-29118800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr22:29101600-29131000	Strong transcription	Dnd41	blood
23	chr22:29102400-29119600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr22:29103400-29118800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr22:29103600-29118800	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr22:29103600-29124800	Weak transcription	GM12878-XiMat	blood
27	chr22:29103600-29132200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr22:29104200-29116600	Weak transcription	Thymus	Thymus
29	chr22:29104400-29116600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr22:29104800-29116600	Weak transcription	Fetal Intestine Large	intestine
31	chr22:29105600-29137200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr22:29106000-29129200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr22:29107600-29116600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr22:29107600-29118600	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr22:29107600-29136800	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr22:29108000-29121000	Weak transcription	K562	blood
37	chr22:29108400-29124400	Weak transcription	Psoas Muscle	Psoas
38	chr22:29108400-29137200	Weak transcription	Right Atrium	heart
39	chr22:29108800-29116600	Weak transcription	Fetal Stomach	stomach
40	chr22:29108800-29120400	Weak transcription	Placenta Amnion	Placenta Amnion
41	chr22:29108800-29126600	Weak transcription	Fetal Muscle Leg	muscle
42	chr22:29108800-29129200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr22:29109000-29116600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr22:29109000-29117600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr22:29109000-29118600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr22:29109000-29129800	Weak transcription	Fetal Lung	lung
47	chr22:29109000-29137000	Weak transcription	HMEC	breast
48	chr22:29109000-29137200	Weak transcription	Liver	Liver
49	chr22:29109000-29137200	Weak transcription	HSMM	muscle
50	chr22:29109200-29116600	Weak transcription	NHLF	lung

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