Variant report

Variant	rs10420264
Chromosome Location	chr19:42438909-42438910
allele	G/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42389371..42391920-chr19:42438453..42441265,2	MCF-7	breast:
2	chr19:42377016..42377922-chr19:42438274..42439260,2	K562	blood:
3	chr19:42376980..42377675-chr19:42438677..42439657,3	MCF-7	breast:
4	chr19:42384855..42393410-chr19:42428364..42439251,22	K562	blood:
5	chr19:42434761..42437338-chr19:42437416..42440186,3	MCF-7	breast:
6	chr19:42375885..42381575-chr19:42432655..42439530,9	K562	blood:
7	chr19:42375846..42378575-chr19:42437686..42441355,5	MCF-7	breast:
8	chr19:42377202..42377808-chr19:42438762..42439328,2	MCF-7	breast:
9	chr19:42385002..42389868-chr19:42433925..42439112,10	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105369	Chromatin interaction
ENSG00000076928	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

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

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

Chromatin state (count:36 , 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	chr19:42437000-42439400	Enhancers	Primary hematopoietic stem cells short term culture	blood
4	chr19:42437200-42439200	Weak transcription	Gastric	stomach
5	chr19:42437600-42439200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr19:42437600-42439800	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr19:42437800-42439200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr19:42437800-42439400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:42437800-42439400	Enhancers	Dnd41	blood
10	chr19:42437800-42440000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr19:42437800-42440600	Enhancers	Primary T cells from cord blood	blood
12	chr19:42437800-42441200	Enhancers	Primary B cells from peripheral blood	blood
13	chr19:42437800-42442600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr19:42437800-42442600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr19:42438000-42439000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr19:42438000-42439200	Enhancers	Primary T cells fromperipheralblood	blood
17	chr19:42438000-42439400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr19:42438000-42439600	Enhancers	Spleen	Spleen
19	chr19:42438000-42439800	Enhancers	Primary B cells from cord blood	blood
20	chr19:42438000-42439800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
21	chr19:42438200-42439000	Enhancers	Primary hematopoietic stem cells	blood
22	chr19:42438200-42439200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr19:42438200-42439400	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr19:42438200-42439400	Enhancers	GM12878-XiMat	blood
25	chr19:42438200-42441800	Enhancers	K562	blood
26	chr19:42438400-42439200	Enhancers	A549	lung
27	chr19:42438400-42439400	Bivalent Enhancer	Fetal Thymus	thymus
28	chr19:42438400-42440800	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr19:42438400-42440800	Enhancers	Esophagus	oesophagus
30	chr19:42438400-42441400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
31	chr19:42438600-42439400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
32	chr19:42438600-42439600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr19:42438600-42441000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:42438800-42439200	Bivalent Enhancer	Thymus	Thymus
35	chr19:42438800-42439800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr19:42438800-42441400	Bivalent Enhancer	Stomach Mucosa	stomach

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