Variant report

Variant	rs10416501
Chromosome Location	chr19:42456602-42456603
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:11)
LncRNA
region (count:0)
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	chr19:42442284..42444187-chr19:42456195..42457752,2	MCF-7	breast:
2	chr19:42362969..42366923-chr19:42454190..42457453,4	K562	blood:
3	chr19:42456140..42457708-chr19:42458791..42460408,2	K562	blood:
4	chr19:42377383..42379799-chr19:42454565..42456876,2	MCF-7	breast:
5	chr19:42363909..42366605-chr19:42455470..42457415,2	MCF-7	breast:
6	chr19:42456024..42458721-chr19:42460619..42462786,2	K562	blood:
7	chr19:42374905..42378139-chr19:42452312..42458975,8	K562	blood:
8	chr19:42443976..42446929-chr19:42455752..42457406,2	MCF-7	breast:
9	chr19:42364389..42367860-chr19:42456039..42459187,3	K562	blood:
10	chr19:42456255..42458695-chr19:42460056..42462256,3	MCF-7	breast:
11	chr19:42374905..42377918-chr19:42453712..42457623,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000105404	Chromatin interaction
ENSG00000105372	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10411814	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10419731	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10420264	0.81[EUR][1000 genomes]
rs10424013	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11083642	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11665965	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11667048	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11668332	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11669448	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11878287	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12971376	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12972751	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12975677	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1864207	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1965727	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2081999	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3745223	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3826707	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61007366	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7246830	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7247727	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7253563	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs735571	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8109192	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs919390	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9304600	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9676662	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9749440	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10416501	RABAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:102 , 50 per page) page: 1 2 3

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	chr19:42455600-42459400	Weak transcription	Liver	Liver
16	chr19:42455800-42461000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr19:42455800-42462400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr19:42456000-42459600	Weak transcription	Brain Anterior Caudate	brain
19	chr19:42456000-42459600	Weak transcription	Lung	lung
20	chr19:42456000-42459600	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr19:42456000-42460000	Weak transcription	Adipose Nuclei	Adipose
22	chr19:42456000-42460200	Weak transcription	Right Ventricle	heart
23	chr19:42456000-42462000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr19:42456200-42458000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:42456200-42458400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr19:42456200-42458800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:42456200-42459000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr19:42456200-42459000	Weak transcription	Fetal Stomach	stomach
29	chr19:42456200-42459200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr19:42456200-42459200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:42456200-42459200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr19:42456200-42459200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:42456200-42459200	Weak transcription	Placenta	Placenta
34	chr19:42456200-42459200	Weak transcription	Spleen	Spleen
35	chr19:42456200-42459400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:42456200-42459400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr19:42456200-42459400	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr19:42456200-42459600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr19:42456200-42459600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr19:42456200-42459600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr19:42456200-42459600	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr19:42456200-42459600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr19:42456200-42459600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:42456200-42459600	Weak transcription	Brain Germinal Matrix	brain
45	chr19:42456200-42459600	Weak transcription	Brain Hippocampus Middle	brain
46	chr19:42456200-42459600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:42456200-42459800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr19:42456200-42459800	Weak transcription	H9 Cell Line	embryonic stem cell
49	chr19:42456200-42459800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr19:42456200-42459800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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