Variant report

Variant	rs1965727
Chromosome Location	chr19:42452305-42452306
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	chr19:42363015..42364647-chr19:42450670..42453103,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105372	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10409822	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10411814	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10414709	0.83[ASN][1000 genomes]
rs10416501	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10419731	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10420264	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10424013	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11083642	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11665965	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11667048	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11668332	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11669448	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11878287	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12971376	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12972751	0.81[EUR][1000 genomes]
rs12975677	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1864207	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2081999	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3745223	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826707	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61007366	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7246830	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7247727	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7253563	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs735571	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8109192	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs919390	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9304600	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9676662	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9749440	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv911777	chr19:42357455-42521108	Bivalent/Poised TSS Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
4	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
5	nsv911780	chr19:42398450-42521108	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
6	nsv911781	chr19:42398450-42542999	Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	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
rs1965727	RABAC1	cis	multi-tissue	Pritchard
rs1965727	RABAC1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42444800-42455600	Weak transcription	K562	blood
2	chr19:42445200-42461000	Weak transcription	Small Intestine	intestine
3	chr19:42445400-42459600	Weak transcription	Gastric	stomach
4	chr19:42445400-42460200	Weak transcription	Pancreas	Pancrea
5	chr19:42445600-42455600	Weak transcription	Right Ventricle	heart
6	chr19:42445600-42462400	Weak transcription	Right Atrium	heart
7	chr19:42446200-42459800	Weak transcription	Aorta	Aorta
8	chr19:42447600-42455800	Weak transcription	Brain Hippocampus Middle	brain
9	chr19:42448000-42452600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr19:42449000-42452800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr19:42449200-42459800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr19:42450000-42455600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr19:42450000-42455600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:42450000-42459200	Weak transcription	Thymus	Thymus
15	chr19:42450200-42455600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:42450800-42455600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr19:42450800-42459800	Weak transcription	Ovary	ovary
18	chr19:42451000-42455600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr19:42451000-42455600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr19:42451000-42455800	Weak transcription	Fetal Stomach	stomach
21	chr19:42451200-42455600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr19:42451200-42455600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr19:42451200-42461600	Weak transcription	Primary hematopoietic stem cells	blood
24	chr19:42451200-42462000	Weak transcription	Primary T cells from cord blood	blood
25	chr19:42451400-42455600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:42451400-42455600	Weak transcription	Spleen	Spleen
27	chr19:42451400-42455800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr19:42451400-42459800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr19:42451600-42452600	Weak transcription	GM12878-XiMat	blood
30	chr19:42451600-42455400	Weak transcription	Primary B cells from cord blood	blood
31	chr19:42451600-42455400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr19:42451600-42459600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr19:42451800-42455400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr19:42451800-42455400	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr19:42451800-42455400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr19:42451800-42455600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr19:42451800-42455600	Weak transcription	Primary T helper cells fromperipheralblood	blood
38	chr19:42451800-42455800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr19:42451800-42459800	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr19:42452000-42452400	Weak transcription	Primary B cells from peripheral blood	blood
41	chr19:42452000-42452400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr19:42452000-42455400	Weak transcription	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links