Variant report

Variant	rs11606580
Chromosome Location	chr11:34976370-34976371
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs10488802	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1117050	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11539202	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11601737	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11605600	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11605972	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11605993	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11606871	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11608116	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1409718	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17347979	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17348697	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17348711	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17349298	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17363135	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17432226	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17433496	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17434808	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17434946	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2217479	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2421744	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3852515	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3852516	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3852517	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs55672020	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55868872	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs55929026	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs55957800	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61734605	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7110461	0.80[EUR][1000 genomes]
rs72912924	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs72912934	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72914758	0.93[EUR][1000 genomes]
rs72924541	0.80[EUR][1000 genomes]
rs72924562	0.80[EUR][1000 genomes]
rs72926580	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72928507	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72930433	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72930443	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72930458	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs72930462	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72930468	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs72930480	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7479823	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7948977	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7950996	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832119	chr11:34815528-35009370	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv2754010	chr11:34940724-35001024	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv430371	chr11:34975067-35111292	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11606580	APIP	cis	Thyroid	GTEx
rs11606580	PDHX	Cis_1M	lymphoblastoid	RTeQTL
rs11606580	APIP	cis	Esophagus Muscularis	GTEx
rs11606580	APIP	cis	Nerve Tibial	GTEx
rs11606580	APIP	cis	Adipose Subcutaneous	GTEx
rs11606580	APIP	cis	Artery Aorta	GTEx
rs11606580	APIP	cis	lung	GTEx
rs11606580	APIP	cis	Heart Left Ventricle	GTEx
rs11606580	APIP	cis	Artery Tibial	GTEx
rs11606580	APIP	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:34938800-34990400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:34939200-35000000	Weak transcription	Thymus	Thymus
3	chr11:34940200-34984800	Weak transcription	Fetal Stomach	stomach
4	chr11:34948000-34990600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr11:34948000-35000400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr11:34948000-35006800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr11:34948200-34997000	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:34948600-34990400	Weak transcription	HUVEC	blood vessel
9	chr11:34949200-34990400	Weak transcription	NHEK	skin
10	chr11:34950400-34991600	Weak transcription	NHLF	lung
11	chr11:34951000-34981400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr11:34951400-34986600	Weak transcription	Fetal Thymus	thymus
13	chr11:34951600-34992000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:34951800-34985000	Weak transcription	Lung	lung
15	chr11:34951800-34988200	Weak transcription	Fetal Intestine Small	intestine
16	chr11:34951800-35000200	Weak transcription	Psoas Muscle	Psoas
17	chr11:34952200-35010800	Weak transcription	Small Intestine	intestine
18	chr11:34952400-34990200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:34954600-34978800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr11:34954600-34986600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr11:34954600-34987800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr11:34954600-34991200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr11:34954800-34988200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr11:34955000-34988200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:34955400-34985200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr11:34955400-34989000	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr11:34955800-34979200	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr11:34955800-34981200	Weak transcription	Brain Anterior Caudate	brain
29	chr11:34955800-34985000	Weak transcription	Placenta	Placenta
30	chr11:34956200-34980800	Weak transcription	Duodenum Mucosa	Duodenum
31	chr11:34956400-34990600	Weak transcription	Fetal Muscle Trunk	muscle
32	chr11:34958200-34978800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr11:34958200-34978800	Weak transcription	Hela-S3	cervix
34	chr11:34958200-34991600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:34958200-34995600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:34959000-34979000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr11:34959000-35019600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr11:34960400-34986600	Weak transcription	K562	blood
39	chr11:34960600-34983200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr11:34960800-34981000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr11:34961400-34990400	Weak transcription	Osteobl	bone
42	chr11:34961800-34997200	Weak transcription	HSMMtube	muscle
43	chr11:34962000-35008200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr11:34962400-34978600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr11:34962600-34998000	Weak transcription	Rectal Smooth Muscle	rectum
46	chr11:34962800-35006600	Weak transcription	Esophagus	oesophagus
47	chr11:34963000-34978600	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr11:34963600-34979000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr11:34963600-34984800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr11:34963600-34986600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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