Variant report

Variant	rs2839998
Chromosome Location	chr22:30729507-30729508
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30729301..30730817-chr22:30750203..30752944,2	K562	blood:
2	chr22:30721780..30724167-chr22:30728041..30729954,3	MCF-7	breast:
3	chr22:30723840..30727994-chr22:30728827..30733130,4	K562	blood:
4	chr22:30728274..30730328-chr22:30731097..30733421,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000099992	Chromatin interaction
ENSG00000099995	Chromatin interaction
ENSG00000187860	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1010324	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11089441	1.00[LWK][hapmap]
rs11089442	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs11089447	0.91[CEU][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.85[AMR][1000 genomes]
rs11089448	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11703385	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11704358	1.00[LWK][hapmap]
rs11705639	0.80[EUR][1000 genomes]
rs12169094	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs12171261	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2074731	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2267154	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2267155	0.91[CEU][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2267156	0.91[CEU][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2283866	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2283870	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2283871	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2299827	0.83[CEU][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs57940170	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs5994294	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs5994305	0.91[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs5994306	0.81[EUR][1000 genomes]
rs5997637	0.91[CEU][hapmap];0.91[MEX][hapmap];0.84[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs5997646	0.91[CEU][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs61583714	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71331235	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7288366	0.91[CEU][hapmap];0.84[GIH][hapmap];0.91[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7289360	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7289384	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7290317	0.91[CEU][hapmap];0.81[CHB][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8141656	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929271	1.00[LWK][hapmap]
rs9619096	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9619098	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9619105	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9620984	0.91[CEU][hapmap];0.81[CHB][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv829171	chr22:30598030-31043578	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv914970	chr22:30619599-30850395	Active TSS Enhancers Genic enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv834174	chr22:30619760-30746915	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv984527	chr22:30698358-30732712	Enhancers Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv3593	chr22:30705980-30751122	Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
6	nsv915818	chr22:30708245-31346302	Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
7	nsv1064350	chr22:30724148-30742125	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	n/a
8	nsv1066179	chr22:30724148-30766466	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2839998	TTC28AS	cis	parietal	SCAN
rs2839998	SYN3	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30723400-30732600	Weak transcription	Right Atrium	heart
2	chr22:30723600-30730400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr22:30723600-30751600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr22:30723800-30742800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr22:30724200-30731200	Weak transcription	Hela-S3	cervix
6	chr22:30724400-30750000	Strong transcription	Thymus	Thymus
7	chr22:30724600-30750200	Strong transcription	Osteobl	bone
8	chr22:30724800-30745200	Strong transcription	NHEK	skin
9	chr22:30724800-30750200	Strong transcription	Fetal Intestine Small	intestine
10	chr22:30725200-30733200	Strong transcription	Fetal Muscle Leg	muscle
11	chr22:30725400-30733400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr22:30725400-30743400	Strong transcription	Fetal Stomach	stomach
13	chr22:30725400-30749600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr22:30725400-30750000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr22:30725600-30733600	Genic enhancers	Placenta	Placenta
16	chr22:30725600-30743600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr22:30725600-30744200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr22:30725600-30750200	Strong transcription	Fetal Intestine Large	intestine
19	chr22:30725800-30732400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr22:30725800-30732800	Strong transcription	Liver	Liver
21	chr22:30725800-30736800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr22:30725800-30740600	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr22:30725800-30742600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr22:30725800-30743200	Strong transcription	Fetal Thymus	thymus
25	chr22:30725800-30748000	Strong transcription	Dnd41	blood
26	chr22:30726000-30743200	Strong transcription	Fetal Lung	lung
27	chr22:30726400-30730400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr22:30726400-30731200	Strong transcription	Left Ventricle	heart
29	chr22:30726400-30740400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr22:30726400-30745400	Strong transcription	HSMM	muscle
31	chr22:30726400-30747000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr22:30726400-30749600	Strong transcription	Fetal Brain Female	brain
33	chr22:30726400-30749600	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr22:30726400-30750200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr22:30726400-30750200	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr22:30726600-30730000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr22:30726600-30732400	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr22:30726600-30732400	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr22:30726600-30733200	Strong transcription	Spleen	Spleen
40	chr22:30726600-30740400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr22:30726600-30743000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
42	chr22:30726600-30743000	Strong transcription	Lung	lung
43	chr22:30726600-30743400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr22:30726600-30743400	Strong transcription	GM12878-XiMat	blood
45	chr22:30726600-30743600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr22:30726600-30744000	Strong transcription	Rectal Smooth Muscle	rectum
47	chr22:30726600-30744600	Strong transcription	Primary T cells from cord blood	blood
48	chr22:30726600-30744600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr22:30726600-30749200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr22:30726600-30749600	Strong transcription	Primary B cells from cord blood	blood

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