Variant report

Variant	rs7253563
Chromosome Location	chr19:42455840-42455841
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42391577..42392478-chr19:42455568..42456267,3	MCF-7	breast:
2	chr19:42296779..42297392-chr19:42455516..42456030,2	K562	blood:
3	chr19:42362969..42366923-chr19:42454190..42457453,4	K562	blood:
4	chr19:42377082..42377816-chr19:42455455..42456477,4	MCF-7	breast:
5	chr19:42452552..42455932-chr19:42460648..42462283,3	K562	blood:
6	chr19:42379366..42382227-chr19:42454447..42456052,2	K562	blood:
7	chr19:42363493..42364002-chr19:42455506..42456182,2	K562	blood:
8	chr19:42377383..42379799-chr19:42454565..42456876,2	MCF-7	breast:
9	chr19:42363909..42366605-chr19:42455470..42457415,2	MCF-7	breast:
10	chr19:42391908..42392858-chr19:42455448..42456435,2	K562	blood:
11	chr19:42374905..42378139-chr19:42452312..42458975,8	K562	blood:
12	chr19:42443976..42446929-chr19:42455752..42457406,2	MCF-7	breast:
13	chr19:42377260..42377774-chr19:42455449..42456424,2	MCF-7	breast:
14	chr19:42376370..42377844-chr19:42455348..42456066,5	K562	blood:
15	chr19:42374905..42377918-chr19:42453712..42457623,5	K562	blood:
16	chr19:42324823..42325616-chr19:42455708..42456330,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105372	Chromatin interaction
ENSG00000105404	Chromatin interaction
ENSG00000105369	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10409822	0.91[ASN][1000 genomes]
rs10411814	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10414709	0.83[ASN][1000 genomes]
rs10416501	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10419731	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10420264	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10424013	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11083642	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11665965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11667048	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11668332	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11669448	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11878287	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12971376	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12972751	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12975677	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1864207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1965727	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2081999	1.00[CEU][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3745223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61007366	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7246830	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7247727	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs735571	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8109192	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs919390	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9304600	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9676662	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9749440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7253563	RABAC1	cis	lymphoblastoid	seeQTL
rs7253563	RABAC1	cis	multi-tissue	Pritchard
rs7253563	RABAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42445200-42461000	Weak transcription	Small Intestine	intestine
2	chr19:42445400-42459600	Weak transcription	Gastric	stomach
3	chr19:42445400-42460200	Weak transcription	Pancreas	Pancrea
4	chr19:42445600-42462400	Weak transcription	Right Atrium	heart
5	chr19:42446200-42459800	Weak transcription	Aorta	Aorta
6	chr19:42449200-42459800	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr19:42450000-42459200	Weak transcription	Thymus	Thymus
8	chr19:42450800-42459800	Weak transcription	Ovary	ovary
9	chr19:42451200-42461600	Weak transcription	Primary hematopoietic stem cells	blood
10	chr19:42451200-42462000	Weak transcription	Primary T cells from cord blood	blood
11	chr19:42451400-42459800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:42451600-42459600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:42451800-42459800	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr19:42452400-42459600	Weak transcription	Fetal Intestine Small	intestine
15	chr19:42455400-42456000	Enhancers	Primary T helper naive cells from peripheral blood	blood
16	chr19:42455400-42456000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr19:42455400-42456200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr19:42455400-42456200	Enhancers	Primary B cells from cord blood	blood
19	chr19:42455400-42456200	Enhancers	Primary B cells from peripheral blood	blood
20	chr19:42455400-42456200	Enhancers	Primary T cells fromperipheralblood	blood
21	chr19:42455400-42456200	Enhancers	Primary T helper cells PMA-I stimulated	--
22	chr19:42455400-42456200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:42455400-42456200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr19:42455400-42456200	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr19:42455400-42456200	Enhancers	Placenta	Placenta
26	chr19:42455400-42456200	Enhancers	Stomach Mucosa	stomach
27	chr19:42455400-42456200	Enhancers	GM12878-XiMat	blood
28	chr19:42455600-42456000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr19:42455600-42456000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr19:42455600-42456000	Enhancers	Adipose Nuclei	Adipose
31	chr19:42455600-42456000	Enhancers	Brain Anterior Caudate	brain
32	chr19:42455600-42456000	Enhancers	Right Ventricle	heart
33	chr19:42455600-42456200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr19:42455600-42456200	Enhancers	H1 Cell Line	embryonic stem cell
35	chr19:42455600-42456200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:42455600-42456200	Active TSS	H9 Cell Line	embryonic stem cell
37	chr19:42455600-42456200	Enhancers	iPS-15b Cell Line	embryonic stem cell
38	chr19:42455600-42456200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr19:42455600-42456200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr19:42455600-42456200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr19:42455600-42456200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
42	chr19:42455600-42456200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr19:42455600-42456200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
44	chr19:42455600-42456200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr19:42455600-42456200	Enhancers	Duodenum Mucosa	Duodenum
46	chr19:42455600-42456200	Enhancers	Fetal Muscle Leg	muscle
47	chr19:42455600-42456200	Enhancers	Fetal Thymus	thymus
48	chr19:42455600-42456200	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr19:42455600-42456200	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr19:42455600-42456200	Enhancers	Spleen	Spleen

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