Variant report

Variant	rs1468090
Chromosome Location	chr22:19815209-19815210
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr22:19806465..19808147-chr22:19814265..19816172,2	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1052988	1.00[ASN][1000 genomes]
rs11089311	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11089314	1.00[ASW][hapmap];0.91[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11089325	1.00[LWK][hapmap]
rs1109436	1.00[ASN][1000 genomes]
rs11702967	1.00[ASN][1000 genomes]
rs11912732	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11913285	1.00[ASW][hapmap];0.83[MEX][hapmap]
rs12165361	1.00[ASN][1000 genomes]
rs12169508	1.00[ASN][1000 genomes]
rs12329964	1.00[ASN][1000 genomes]
rs12485043	1.00[ASN][1000 genomes]
rs17534001	1.00[ASN][1000 genomes]
rs3196628	1.00[ASN][1000 genomes]
rs55812801	1.00[ASN][1000 genomes]
rs62222095	1.00[ASN][1000 genomes]
rs62223685	1.00[ASN][1000 genomes]
rs62223687	1.00[ASN][1000 genomes]
rs62223688	1.00[ASN][1000 genomes]
rs7288631	1.00[ASN][1000 genomes]
rs73150820	1.00[ASN][1000 genomes]
rs73379955	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73379972	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs737861	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9306235	1.00[LWK][hapmap]
rs9332377	1.00[ASN][1000 genomes]
rs9618723	1.00[ASN][1000 genomes]
rs9618724	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv588216	chr22:19073612-19826640	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
2	esv1792516	chr22:19578312-20314496	Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	195 gene(s)	inside rSNPs	diseases
3	nsv914279	chr22:19638044-19954458	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases
4	esv1818018	chr22:19674772-20313261	Flanking Bivalent TSS/Enh Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	193 gene(s)	inside rSNPs	diseases
5	nsv828938	chr22:19678592-20311988	Strong transcription Genic enhancers Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	192 gene(s)	inside rSNPs	diseases
6	nsv828939	chr22:19683555-20311988	Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	192 gene(s)	inside rSNPs	diseases
7	nsv1064992	chr22:19691720-20246906	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
8	nsv834129	chr22:19693140-19906591	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv914288	chr22:19698129-19914854	Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
10	esv1826873	chr22:19726464-20313261	Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
11	nsv914292	chr22:19730592-19872009	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
12	nsv914293	chr22:19730592-19881556	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
13	nsv588237	chr22:19749525-20306993	Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
14	nsv482455	chr22:19758291-19932709	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
15	nsv914296	chr22:19766782-19921003	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
16	nsv1065963	chr22:19779317-20027562	Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
17	nsv544580	chr22:19779317-20027562	Genic enhancers Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
18	nsv914298	chr22:19785006-19879637	Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
19	nsv914299	chr22:19790308-19879637	Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
20	nsv914300	chr22:19802779-19889423	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
21	esv1800885	chr22:19814259-19830310	Weak transcription Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1468090	C22orf29	Cis_1M	lymphoblastoid	RTeQTL
rs1468090	RTN4R	cis	cerebellum	SCAN
rs1468090	TXNRD2	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:19794400-19831000	Weak transcription	Aorta	Aorta
2	chr22:19799400-19838800	Weak transcription	Ovary	ovary
3	chr22:19800400-19820800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr22:19802000-19823800	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr22:19808600-19830400	Weak transcription	Primary T cells from cord blood	blood
6	chr22:19809200-19830000	Weak transcription	Right Atrium	heart
7	chr22:19810400-19830000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr22:19811000-19819800	Weak transcription	Right Ventricle	heart
9	chr22:19812000-19829400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr22:19812400-19820200	Weak transcription	Primary B cells from peripheral blood	blood
11	chr22:19812600-19816600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr22:19812600-19820000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr22:19812800-19820400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr22:19812800-19820400	Weak transcription	HMEC	breast
15	chr22:19812800-19828000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr22:19812800-19828400	Weak transcription	Fetal Intestine Small	intestine
17	chr22:19813600-19827800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr22:19813800-19815600	Enhancers	HepG2	liver
19	chr22:19814000-19815600	Weak transcription	Fetal Stomach	stomach
20	chr22:19814400-19815800	Weak transcription	Primary B cells from cord blood	blood
21	chr22:19814400-19819600	Weak transcription	Dnd41	blood
22	chr22:19814400-19820200	Weak transcription	Esophagus	oesophagus
23	chr22:19814400-19829800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr22:19814600-19819800	Weak transcription	Fetal Thymus	thymus
25	chr22:19814600-19819800	Weak transcription	Thymus	Thymus
26	chr22:19814800-19816000	Flanking Active TSS	K562	blood
27	chr22:19815200-19815400	Enhancers	A549	lung
28	chr22:19815200-19831200	Weak transcription	NHDF-Ad	bronchial

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