Variant report

Variant	rs11070290
Chromosome Location	chr15:41014720-41014721
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1051482	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11852479	0.82[AMR][1000 genomes]
rs11855517	0.84[AMR][1000 genomes]
rs11855641	0.82[EUR][1000 genomes]
rs12148185	0.84[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12898552	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12908443	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12910784	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2010300	0.86[EUR][1000 genomes]
rs2289219	0.90[EUR][1000 genomes]
rs2304583	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412545	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2899000	0.83[EUR][1000 genomes]
rs34621344	0.86[EUR][1000 genomes]
rs34988257	0.90[EUR][1000 genomes]
rs36094699	0.87[AMR][1000 genomes]
rs3759796	0.85[EUR][1000 genomes]
rs4457966	0.82[AMR][1000 genomes]
rs45592734	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5030783	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62018584	0.82[EUR][1000 genomes]
rs62019934	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs8031427	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8038396	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
5	nsv527234	chr15:40987725-41031686	Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs11070290	RP11-111A22.1	cis	Esophagus Muscularis	GTEx
rs11070290	RP11-111A22.1	cis	Artery Tibial	GTEx
rs11070290	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs11070290	C15orf57	cis	Stomach	GTEx
rs11070290	RAD51	Cis_1M	lymphoblastoid	RTeQTL
rs11070290	RAD51	cis	multi-tissue	Pritchard
rs11070290	C15orf57	cis	lung	GTEx
rs11070290	C15orf57	cis	Nerve Tibial	GTEx
rs11070290	CCDC32	Cis_1M	lymphoblastoid	RTeQTL
rs11070290	C15orf57	cis	Artery Tibial	GTEx
rs11070290	C15orf57	cis	Artery Aorta	GTEx
rs11070290	C15orf57	cis	Esophagus Muscularis	GTEx
rs11070290	CCDC32	cis	multi-tissue	Pritchard
rs11070290	RP11-111A22.1	cis	lung	GTEx
rs11070290	ZFYVE19	cis	multi-tissue	Pritchard
rs11070290	C15orf57	cis	Esophagus Mucosa	GTEx
rs11070290	C15orf57	cis	Adipose Subcutaneous	GTEx
rs11070290	ZFYVE19	Cis_1M	lymphoblastoid	RTeQTL
rs11070290	C15orf57	cis	Muscle Skeletal	GTEx

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40988000-41030000	Weak transcription	Pancreas	Pancrea
2	chr15:40988200-41028600	Weak transcription	Spleen	Spleen
3	chr15:40988400-41020600	Weak transcription	Placenta	Placenta
4	chr15:40988400-41020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:40988400-41021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:40988400-41021800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:40988400-41027200	Weak transcription	Primary B cells from cord blood	blood
8	chr15:40988400-41031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:40988600-41018400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:40988600-41021400	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:40988600-41021400	Weak transcription	Fetal Brain Female	brain
12	chr15:40988800-41020600	Weak transcription	Primary T cells from cord blood	blood
13	chr15:40988800-41021600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr15:40988800-41021800	Weak transcription	Fetal Kidney	kidney
15	chr15:40989000-41018000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:40990200-41016800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:40990200-41016800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:40990600-41015000	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:40990600-41022600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:40990800-41016000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr15:40992000-41016600	Strong transcription	Dnd41	blood
22	chr15:40993200-41025800	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr15:40994000-41020600	Weak transcription	HSMM	muscle
24	chr15:40997800-41020800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:40998200-41023200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:40998800-41038000	Weak transcription	Stomach Mucosa	stomach
27	chr15:40999000-41027600	Weak transcription	Gastric	stomach
28	chr15:40999200-41021600	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr15:41000000-41026000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr15:41001400-41020800	Weak transcription	NHDF-Ad	bronchial
31	chr15:41001600-41020600	Weak transcription	NH-A	brain
32	chr15:41002000-41019600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:41002000-41021400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr15:41002200-41021600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr15:41002800-41019400	Weak transcription	Fetal Stomach	stomach
36	chr15:41003200-41021800	Weak transcription	Brain Germinal Matrix	brain
37	chr15:41003600-41021800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr15:41003800-41015600	Weak transcription	HMEC	breast
39	chr15:41003800-41023800	Weak transcription	Fetal Lung	lung
40	chr15:41004000-41021600	Weak transcription	Osteobl	bone
41	chr15:41004600-41021000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr15:41004800-41020600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr15:41004800-41022000	Weak transcription	A549	lung
44	chr15:41004800-41023400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr15:41005000-41019600	Weak transcription	Primary hematopoietic stem cells	blood
46	chr15:41005000-41021400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr15:41005800-41016600	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr15:41006000-41014800	Strong transcription	Fetal Thymus	thymus
49	chr15:41006000-41015400	Strong transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:41006400-41021800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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