Variant report

Variant	rs10409822
Chromosome Location	chr19:42434050-42434051
allele	C/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:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42361079..42367934-chr19:42431466..42436133,8	K562	blood:
2	chr19:42411008..42413739-chr19:42433473..42435973,2	K562	blood:
3	chr19:42384855..42393410-chr19:42428364..42439251,22	K562	blood:
4	chr19:42431551..42433340-chr19:42433915..42436394,2	MCF-7	breast:
5	chr19:42375885..42381575-chr19:42432655..42439530,9	K562	blood:
6	chr19:42433284..42435979-chr19:42448228..42450918,2	K562	blood:
7	chr19:42396004..42397685-chr19:42433776..42436309,2	K562	blood:
8	chr19:42430426..42435985-chr19:42461209..42463660,4	K562	blood:
9	chr19:42382327..42390135-chr19:42429723..42437438,12	MCF-7	breast:
10	chr19:42385002..42389868-chr19:42433925..42439112,10	K562	blood:
11	chr19:42398480..42400174-chr19:42432062..42434996,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ARHGEF1-2	chr19:42433807-42434302	NONHSAT066503

No data

Variant related genes	Relation type
ENSG00000105404	Chromatin interaction
ENSG00000076928	Chromatin interaction
ENSG00000105369	Chromatin interaction
ENSG00000105372	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10411814	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10419731	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10420264	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10424013	0.91[ASN][1000 genomes]
rs11083642	0.88[ASN][1000 genomes]
rs11665965	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11667048	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11668332	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11669448	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11878287	0.88[ASN][1000 genomes]
rs12971376	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12975677	0.82[ASN][1000 genomes]
rs1864207	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1965727	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2081999	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3745223	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3826707	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61007366	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7246830	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs7247727	0.88[ASN][1000 genomes]
rs7253563	0.91[ASN][1000 genomes]
rs735571	0.84[ASN][1000 genomes]
rs8109192	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs919390	0.84[ASN][1000 genomes]
rs9749440	0.84[AMR][1000 genomes];0.92[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
rs10409822	RABAC1	Cis_1M	lymphoblastoid	RTeQTL
rs10409822	RABAC1	cis	multi-tissue	Pritchard

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42432400-42434600	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
2	chr19:42432800-42434200	ZNF genes & repeats	Lung	lung
3	chr19:42433000-42435000	Flanking Active TSS	K562	blood
4	chr19:42433200-42441400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
5	chr19:42433400-42434200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
6	chr19:42433400-42434200	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr19:42433400-42434600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:42433400-42434800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr19:42433400-42435000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
10	chr19:42433400-42435200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr19:42433400-42435400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
12	chr19:42433600-42434200	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:42433600-42434400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr19:42433600-42434600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
15	chr19:42433600-42434600	Bivalent Enhancer	Duodenum Mucosa	Duodenum
16	chr19:42433600-42434600	Enhancers	Gastric	stomach
17	chr19:42433600-42434600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
18	chr19:42433600-42434600	Bivalent Enhancer	GM12878-XiMat	blood
19	chr19:42433600-42434800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
20	chr19:42433600-42434800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr19:42433600-42435000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr19:42433600-42435000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr19:42433600-42435000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr19:42433600-42435000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr19:42433600-42435200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:42433600-42435400	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr19:42433600-42435600	Bivalent Enhancer	Thymus	Thymus
28	chr19:42433600-42435800	Bivalent Enhancer	Fetal Thymus	thymus
29	chr19:42433600-42444000	Weak transcription	Right Atrium	heart
30	chr19:42433800-42434200	Bivalent Enhancer	Brain Germinal Matrix	brain
31	chr19:42433800-42434800	Genic enhancers	Dnd41	blood
32	chr19:42434000-42434400	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
33	chr19:42434000-42434400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr19:42434000-42434400	Weak transcription	Pancreas	Pancrea
35	chr19:42434000-42434800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr19:42434000-42434800	Enhancers	Spleen	Spleen
37	chr19:42434000-42435200	Bivalent Enhancer	Primary B cells from cord blood	blood
38	chr19:42434000-42436000	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr19:42434000-42436400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell

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