Variant report

Variant	rs11669448
Chromosome Location	chr19:42436623-42436624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42429855..42432360-chr19:42434801..42438430,3	MCF-7	breast:
2	chr19:42417890..42419536-chr19:42436129..42438238,2	MCF-7	breast:
3	chr19:42384855..42393410-chr19:42428364..42439251,22	K562	blood:
4	chr19:42375885..42381575-chr19:42432655..42439530,9	K562	blood:
5	chr19:42435516..42438496-chr7:44152136..44154138,2	K562	blood:
6	chr19:42434761..42437338-chr19:42437416..42440186,3	MCF-7	breast:
7	chr19:42392209..42393764-chr19:42436323..42438762,2	MCF-7	breast:
8	chr19:42426185..42428300-chr19:42435310..42438359,3	MCF-7	breast:
9	chr19:42364529..42366341-chr19:42436267..42438526,2	K562	blood:
10	chr19:42382327..42390135-chr19:42429723..42437438,12	MCF-7	breast:
11	chr19:42400210..42402238-chr19:42436524..42438130,2	MCF-7	breast:
12	chr19:42385002..42389868-chr19:42433925..42439112,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000076928	Chromatin interaction
ENSG00000105369	Chromatin interaction
ENSG00000105372	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10409822	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10411814	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10414709	0.82[ASN][1000 genomes]
rs10416501	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10419731	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10420264	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10424013	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11083642	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11665965	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11667048	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11668332	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11878287	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12971376	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12975677	0.92[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1864207	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1965727	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2081999	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3745223	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3826707	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61007366	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7246830	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7247727	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7253563	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs735571	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8109192	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs919390	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9304600	0.84[EUR][1000 genomes]
rs9676662	0.87[EUR][1000 genomes]
rs9749440	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[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
rs11669448	RABAC1	cis	multi-tissue	Pritchard
rs11669448	RABAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42433200-42441400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
2	chr19:42433600-42444000	Weak transcription	Right Atrium	heart
3	chr19:42434600-42436800	Weak transcription	Pancreas	Pancrea
4	chr19:42434800-42437800	Weak transcription	Dnd41	blood
5	chr19:42434800-42438200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:42434800-42438800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr19:42435000-42437800	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr19:42435000-42438400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr19:42435200-42437800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr19:42435400-42438200	Weak transcription	K562	blood
11	chr19:42435400-42438400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr19:42435600-42437200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
13	chr19:42435600-42437800	Weak transcription	Primary T cells from cord blood	blood
14	chr19:42435600-42438000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr19:42435600-42438000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr19:42435600-42438200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr19:42435800-42438000	Weak transcription	Primary B cells from cord blood	blood
18	chr19:42435800-42438600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr19:42436000-42436800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:42436000-42437600	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
21	chr19:42436000-42437800	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr19:42436200-42437000	Bivalent Enhancer	A549	lung
23	chr19:42436200-42437400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
24	chr19:42436200-42437600	Bivalent Enhancer	Fetal Muscle Leg	muscle
25	chr19:42436200-42437800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr19:42436400-42436800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr19:42436400-42437000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
28	chr19:42436400-42437200	Bivalent Enhancer	Fetal Lung	lung
29	chr19:42436400-42437200	Bivalent Enhancer	Placenta	Placenta
30	chr19:42436400-42437200	Enhancers	Gastric	stomach
31	chr19:42436400-42437400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr19:42436400-42437400	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr19:42436400-42437600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr19:42436400-42438000	Bivalent Enhancer	Fetal Stomach	stomach
35	chr19:42436600-42436800	Flanking Bivalent TSS/Enh	Osteobl	bone
36	chr19:42436600-42437000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
37	chr19:42436600-42437000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
38	chr19:42436600-42437200	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr19:42436600-42437400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:42436600-42438200	Bivalent Enhancer	Brain Germinal Matrix	brain

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