Variant report

Variant	rs7250787
Chromosome Location	chr19:42367621-42367622
allele	A/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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:42346899..42349395-chr19:42366337..42367958,2	K562	blood:
2	chr19:42362804..42368897-chr19:42386582..42393421,16	MCF-7	breast:
3	chr19:42366555..42368141-chr19:42405130..42408050,2	K562	blood:
4	chr19:42367000..42368909-chr19:42375795..42378988,3	MCF-7	breast:
5	chr19:42367135..42368961-chr19:42460272..42462681,2	K562	blood:
6	chr19:42343167..42345193-chr19:42366399..42369039,2	K562	blood:
7	chr19:42365213..42368096-chr19:42429393..42431288,2	K562	blood:
8	chr19:42366028..42368892-chr19:42439399..42440962,2	MCF-7	breast:
9	chr19:42366833..42368695-chr19:42529044..42531497,2	K562	blood:
10	chr19:42311416..42313552-chr19:42366859..42369350,2	MCF-7	breast:
11	chr19:42366038..42367665-chr19:42439832..42441415,2	K562	blood:
12	chr19:42366833..42368938-chr19:42528843..42531497,3	K562	blood:
13	chr19:42362135..42368129-chr19:42461941..42464761,7	MCF-7	breast:
14	chr19:42361079..42367934-chr19:42431466..42436133,8	K562	blood:
15	chr19:42362252..42368846-chr19:42460307..42464966,15	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000183103	Chromatin interaction
ENSG00000105404	Chromatin interaction
ENSG00000142025	Chromatin interaction
ENSG00000170956	Chromatin interaction
ENSG00000076928	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10404939	0.82[ASN][1000 genomes]
rs10405900	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10414356	0.83[ASN][1000 genomes]
rs10414823	0.84[AFR][1000 genomes]
rs10415452	0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10417985	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10500284	0.84[ASN][1000 genomes]
rs12461099	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12461131	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12976571	0.82[ASN][1000 genomes]
rs12984383	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1366610	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1428922	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1457144	0.82[ASN][1000 genomes]
rs1870093	0.81[ASN][1000 genomes]
rs2075749	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2075750	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2075752	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2075754	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290695	0.82[ASN][1000 genomes]
rs2305809	0.84[ASN][1000 genomes]
rs28824227	0.82[AFR][1000 genomes]
rs3786536	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3786538	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3810153	0.86[ASN][1000 genomes]
rs3922888	0.83[ASN][1000 genomes]
rs4130852	0.83[ASN][1000 genomes]
rs4803511	0.83[ASN][1000 genomes]
rs4803512	0.83[ASN][1000 genomes]
rs58857981	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6508999	0.82[AFR][1000 genomes]
rs6509001	0.84[ASN][1000 genomes]
rs7248641	0.82[ASN][1000 genomes]
rs7254214	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7257666	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7258163	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7259596	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7259967	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73549152	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8102670	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8104958	0.82[ASN][1000 genomes]
rs8113780	0.82[ASN][1000 genomes]
rs873282	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs882520	0.87[ASN][1000 genomes]
rs891167	0.82[AMR][1000 genomes]
rs930102	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[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	nsv1061878	chr19:42325490-42416056	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv911776	chr19:42343526-42416056	Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
4	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
5	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
6	nsv911778	chr19:42358362-42416056	Strong transcription Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7250787	RPS19	cis	Esophagus Muscularis	GTEx
rs7250787	RABAC1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42364600-42367800	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
2	chr19:42364600-42367800	Transcr. at gene 5' and 3'	A549	lung
3	chr19:42364600-42368800	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr19:42364600-42369000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr19:42364800-42367800	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr19:42364800-42367800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
7	chr19:42364800-42369000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:42365200-42368800	Genic enhancers	Spleen	Spleen
9	chr19:42365200-42369600	Transcr. at gene 5' and 3'	Hela-S3	cervix
10	chr19:42365400-42367800	Genic enhancers	Primary monocytes fromperipheralblood	blood
11	chr19:42365400-42369200	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
12	chr19:42365400-42369800	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
13	chr19:42365400-42374800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr19:42365400-42375000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr19:42365400-42376200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr19:42365400-42376600	Genic enhancers	Primary B cells from peripheral blood	blood
17	chr19:42365600-42367800	Genic enhancers	Esophagus	oesophagus
18	chr19:42365600-42367800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr19:42365600-42367800	Genic enhancers	Left Ventricle	heart
20	chr19:42365600-42368000	Genic enhancers	Placenta	Placenta
21	chr19:42365600-42368400	Genic enhancers	Brain Cingulate Gyrus	brain
22	chr19:42365600-42368400	Genic enhancers	Stomach Mucosa	stomach
23	chr19:42365600-42368800	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:42365600-42368800	Genic enhancers	Gastric	stomach
25	chr19:42365600-42368800	Genic enhancers	Lung	lung
26	chr19:42365600-42369600	Genic enhancers	Pancreas	Pancrea
27	chr19:42365600-42370000	Genic enhancers	Fetal Muscle Leg	muscle
28	chr19:42365600-42370800	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr19:42365600-42374600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr19:42365600-42374800	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr19:42365800-42367800	Genic enhancers	Primary B cells from cord blood	blood
32	chr19:42365800-42367800	Genic enhancers	Primary hematopoietic stem cells	blood
33	chr19:42365800-42367800	Genic enhancers	Adipose Nuclei	Adipose
34	chr19:42365800-42367800	Genic enhancers	Brain Angular Gyrus	brain
35	chr19:42365800-42367800	Genic enhancers	Brain Anterior Caudate	brain
36	chr19:42365800-42367800	Genic enhancers	Brain Hippocampus Middle	brain
37	chr19:42365800-42368800	Genic enhancers	Fetal Stomach	stomach
38	chr19:42365800-42368800	Genic enhancers	Rectal Mucosa Donor 31	rectum
39	chr19:42365800-42368800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
40	chr19:42365800-42369000	Strong transcription	Pancreatic Islets	Pancreatic Islet
41	chr19:42365800-42369000	Genic enhancers	Rectal Mucosa Donor 29	rectum
42	chr19:42365800-42369200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr19:42365800-42369600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr19:42365800-42370800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
45	chr19:42365800-42374600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr19:42365800-42374800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr19:42365800-42375000	Genic enhancers	Fetal Intestine Small	intestine
48	chr19:42366000-42367800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr19:42366000-42369000	Genic enhancers	NHDF-Ad	bronchial
50	chr19:42366000-42369200	Genic enhancers	Stomach Smooth Muscle	stomach

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