Variant report

Variant	rs10770039
Chromosome Location	chr11:9587187-9587188
allele	C/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	chr11:9586720..9588950-chr11:9633664..9636381,2	MCF-7	breast:
2	chr11:9571631..9575583-chr11:9586034..9589231,7	K562	blood:
3	chr11:9555259..9558705-chr11:9585485..9589925,6	MCF-7	breast:
4	chr11:9481046..9484761-chr11:9586134..9589089,3	K562	blood:
5	chr11:9571631..9575267-chr11:9586177..9589837,7	K562	blood:
6	chr11:9480505..9483830-chr11:9585814..9588292,3	MCF-7	breast:
7	chr11:9586513..9589428-chr11:9634913..9638092,4	K562	blood:
8	chr11:9482098..9486375-chr11:9587030..9591762,7	K562	blood:
9	chr11:9586141..9589428-chr11:9634451..9638092,8	K562	blood:
10	chr11:9554695..9557077-chr11:9586375..9588015,2	MCF-7	breast:
11	chr11:9568845..9571687-chr11:9584887..9588647,3	MCF-7	breast:
12	chr11:9555332..9556950-chr11:9587020..9589560,2	K562	blood:
13	chr11:9550967..9553187-chr11:9587161..9589570,2	K562	blood:
14	chr11:9548940..9552769-chr11:9586407..9589954,6	MCF-7	breast:
15	chr11:9586732..9588920-chr4:24377644..24379144,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000166478	Chromatin interaction
ENSG00000268403	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs4370932	0.81[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs7937639	0.91[CEU][hapmap];0.81[GIH][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427882	chr11:9431600-9626580	Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv553467	chr11:9518551-9648721	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10770039	SYT9	cis	cerebellum	SCAN
rs10770039	OR56A4	cis	cerebellum	SCAN
rs10770039	DKK3	cis	cerebellum	SCAN
rs10770039	SNORA45	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9566400-9587400	Weak transcription	Psoas Muscle	Psoas
2	chr11:9573800-9587800	Weak transcription	Gastric	stomach
3	chr11:9579000-9590200	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr11:9583000-9590200	Weak transcription	Primary T cells from cord blood	blood
5	chr11:9584200-9594400	Enhancers	Stomach Mucosa	stomach
6	chr11:9584200-9594400	Weak transcription	Spleen	Spleen
7	chr11:9585000-9589600	Weak transcription	Primary B cells from cord blood	blood
8	chr11:9585200-9587400	Weak transcription	Fetal Muscle Leg	muscle
9	chr11:9585200-9590800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr11:9585200-9593600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr11:9585200-9594400	Weak transcription	Esophagus	oesophagus
12	chr11:9585200-9594400	Weak transcription	Lung	lung
13	chr11:9585400-9587200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:9586000-9591600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr11:9586200-9587600	Enhancers	Fetal Heart	heart
16	chr11:9586200-9590400	Enhancers	Fetal Lung	lung
17	chr11:9586200-9590600	Enhancers	Hela-S3	cervix
18	chr11:9586200-9590600	Enhancers	NHLF	lung
19	chr11:9586400-9587200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr11:9586400-9587200	Enhancers	A549	lung
21	chr11:9586400-9587200	Enhancers	GM12878-XiMat	blood
22	chr11:9586400-9587200	Enhancers	HepG2	liver
23	chr11:9586400-9587200	Enhancers	NHEK	skin
24	chr11:9586400-9587600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:9586400-9587600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:9586400-9589800	Enhancers	HMEC	breast
27	chr11:9586400-9589800	Enhancers	Osteobl	bone
28	chr11:9586400-9590000	Enhancers	Placenta Amnion	Placenta Amnion
29	chr11:9586400-9594200	Enhancers	Fetal Intestine Small	intestine
30	chr11:9586600-9587200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr11:9586600-9587200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr11:9586600-9587200	Enhancers	K562	blood
33	chr11:9586600-9587200	Enhancers	NH-A	brain
34	chr11:9586600-9587400	Enhancers	iPS-20b Cell Line	embryonic stem cell
35	chr11:9586600-9587400	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr11:9586600-9587400	Enhancers	Stomach Smooth Muscle	stomach
37	chr11:9586600-9587800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr11:9586600-9588000	Enhancers	Left Ventricle	heart
39	chr11:9586600-9588000	Enhancers	Pancreas	Pancrea
40	chr11:9586600-9588200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:9586600-9588200	Enhancers	Aorta	Aorta
42	chr11:9586600-9588200	Enhancers	Colonic Mucosa	Colon
43	chr11:9586600-9588200	Enhancers	Ovary	ovary
44	chr11:9586600-9588200	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr11:9586600-9588200	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr11:9586600-9588200	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr11:9586600-9588400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr11:9586600-9588600	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr11:9586600-9588600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr11:9586600-9588600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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