Variant report

Variant	rs568959
Chromosome Location	chr11:74037083-74037084
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1063807	0.96[ASN][1000 genomes]
rs10793071	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs10898977	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10898978	0.90[ASN][1000 genomes]
rs10898979	0.88[ASN][1000 genomes]
rs10898982	0.81[ASN][1000 genomes]
rs12364246	0.95[ASN][1000 genomes]
rs12365592	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12804647	0.80[ASN][1000 genomes]
rs1941817	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3193507	0.96[ASN][1000 genomes]
rs3867269	0.92[ASN][1000 genomes]
rs3894651	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4306310	0.95[ASN][1000 genomes]
rs4641511	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs513678	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55660813	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61901471	0.81[ASN][1000 genomes]
rs627354	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs634243	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs642884	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7106149	0.84[ASN][1000 genomes]
rs7106827	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7121767	0.82[ASN][1000 genomes]
rs7129306	0.83[ASN][1000 genomes]
rs7130795	0.83[ASN][1000 genomes]
rs752577	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7931026	0.94[ASN][1000 genomes]
rs7943938	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7947390	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[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	esv2757451	chr11:73842609-74545888	Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	esv2759837	chr11:73842609-74557597	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	esv34979	chr11:73878688-74533452	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
4	esv2758277	chr11:73887567-74557597	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
5	nsv825994	chr11:73936667-74534455	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	83 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs568959	RP11-702H23.4	cis	Thyroid	GTEx
rs568959	HNRNPA1P40	cis	Thyroid	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:74028800-74038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr11:74030800-74037200	Weak transcription	Aorta	Aorta
3	chr11:74031200-74071200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:74033200-74047200	Weak transcription	Primary B cells from peripheral blood	blood
5	chr11:74033600-74040600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr11:74035000-74038400	Enhancers	Fetal Muscle Leg	muscle
7	chr11:74035400-74038000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr11:74035400-74038000	Enhancers	Psoas Muscle	Psoas
9	chr11:74035400-74038000	Enhancers	HSMMtube	muscle
10	chr11:74036200-74038200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr11:74036200-74038800	Enhancers	Fetal Brain Male	brain
12	chr11:74036400-74037600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr11:74036400-74037600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr11:74036400-74037600	Enhancers	Brain Angular Gyrus	brain
15	chr11:74036400-74037800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:74036400-74037800	Enhancers	NHDF-Ad	bronchial
17	chr11:74036400-74038000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr11:74036400-74038000	Enhancers	Osteobl	bone
19	chr11:74036400-74038200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr11:74036400-74038200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr11:74036400-74038400	Enhancers	Brain Hippocampus Middle	brain
22	chr11:74036400-74038400	Enhancers	Fetal Heart	heart
23	chr11:74036400-74038400	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr11:74036600-74037200	Enhancers	Stomach Mucosa	stomach
25	chr11:74036600-74037400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:74036600-74037400	Enhancers	Duodenum Mucosa	Duodenum
27	chr11:74036600-74037400	Enhancers	Placenta	Placenta
28	chr11:74036600-74037400	Enhancers	NHLF	lung
29	chr11:74036600-74037600	Enhancers	Brain Cingulate Gyrus	brain
30	chr11:74036600-74037600	Enhancers	Brain Substantia Nigra	brain
31	chr11:74036600-74037600	Enhancers	Esophagus	oesophagus
32	chr11:74036600-74037600	Enhancers	Fetal Intestine Large	intestine
33	chr11:74036600-74037600	Enhancers	Fetal Intestine Small	intestine
34	chr11:74036600-74037600	Enhancers	Pancreas	Pancrea
35	chr11:74036600-74037600	Enhancers	HSMM	muscle
36	chr11:74036600-74037800	Enhancers	Brain Anterior Caudate	brain
37	chr11:74036600-74037800	Enhancers	NH-A	brain
38	chr11:74036600-74038000	Enhancers	Brain Germinal Matrix	brain
39	chr11:74036600-74038000	Enhancers	Duodenum Smooth Muscle	Duodenum
40	chr11:74036600-74038000	Enhancers	Gastric	stomach
41	chr11:74036600-74038000	Enhancers	Rectal Smooth Muscle	rectum
42	chr11:74036600-74038000	Enhancers	Right Atrium	heart
43	chr11:74036600-74038200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr11:74036600-74038200	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr11:74036600-74038200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
46	chr11:74036600-74038200	Enhancers	Colon Smooth Muscle	Colon
47	chr11:74036600-74038200	Enhancers	Fetal Lung	lung
48	chr11:74036600-74038200	Enhancers	Left Ventricle	heart
49	chr11:74036600-74038200	Enhancers	Ovary	ovary
50	chr11:74036600-74038200	Enhancers	Spleen	Spleen

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