Variant report

Variant	rs11197000
Chromosome Location	chr10:116701469-116701470
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 105 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10160015	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10444099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1045657	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10490908	1.00[JPT][hapmap]
rs10510008	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10885631	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10885632	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10885633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885634	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10885636	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10885637	1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885638	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10885639	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196983	0.86[ASN][1000 genomes]
rs11196984	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs11196989	0.86[ASN][1000 genomes]
rs11196991	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11196999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197005	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197006	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11197007	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197010	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11197011	0.95[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11197023	0.95[ASN][1000 genomes]
rs12098332	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12246008	0.95[ASN][1000 genomes]
rs12265048	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12269261	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12761122	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12764662	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12772737	0.95[ASN][1000 genomes]
rs12774597	0.95[ASN][1000 genomes]
rs12775180	1.00[JPT][hapmap]
rs12779231	0.95[ASN][1000 genomes]
rs17092542	1.00[JPT][hapmap]
rs17721283	1.00[JPT][hapmap]
rs17721905	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17722042	0.95[ASN][1000 genomes]
rs17794346	1.00[JPT][hapmap]
rs17795104	0.95[ASN][1000 genomes]
rs17795212	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1966384	1.00[JPT][hapmap]
rs2095379	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2105001	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2420070	0.86[ASN][1000 genomes]
rs34170154	0.95[ASN][1000 genomes]
rs34434610	0.95[ASN][1000 genomes]
rs34453431	0.95[ASN][1000 genomes]
rs34461950	0.87[ASN][1000 genomes]
rs35501899	0.95[ASN][1000 genomes]
rs35811923	0.95[ASN][1000 genomes]
rs3931556	0.84[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61869271	0.95[ASN][1000 genomes]
rs61869272	0.95[ASN][1000 genomes]
rs61869274	0.95[ASN][1000 genomes]
rs61869275	0.95[ASN][1000 genomes]
rs6585302	0.86[ASN][1000 genomes]
rs6585306	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6585309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6585310	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6585311	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6585313	0.95[ASN][1000 genomes]
rs7071789	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7071812	0.92[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7072356	1.00[JPT][hapmap]
rs7074729	1.00[JPT][hapmap]
rs7075888	1.00[JPT][hapmap]
rs7079234	0.95[ASN][1000 genomes]
rs7085964	0.95[ASN][1000 genomes]
rs7093282	0.83[ASN][1000 genomes]
rs7093330	0.95[ASN][1000 genomes]
rs7094072	1.00[JPT][hapmap]
rs7097580	0.95[ASN][1000 genomes]
rs7099565	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7099590	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7099779	1.00[ASN][1000 genomes]
rs7100026	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7100159	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7100894	0.86[ASN][1000 genomes]
rs72836518	0.95[ASN][1000 genomes]
rs749649	1.00[JPT][hapmap]
rs7895551	1.00[JPT][hapmap]
rs7898249	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7904605	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7908069	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7908464	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7909566	1.00[JPT][hapmap]
rs7909657	1.00[JPT][hapmap]
rs7917523	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7923295	1.00[JPT][hapmap]
rs881192	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs968848	0.95[ASN][1000 genomes]
rs968849	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949138	chr10:116311531-116874477	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1038050	chr10:116315109-116895719	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv533027	chr10:116344641-116856352	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv3435429	chr10:116394152-117006347	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv831996	chr10:116601552-116772968	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Flanking 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	11 gene(s)	inside rSNPs	diseases
6	nsv1039002	chr10:116643095-116879483	Active TSS Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	esv2761634	chr10:116643095-116879495	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv1045654	chr10:116654574-116879483	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv1043242	chr10:116655057-116883386	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
10	nsv831997	chr10:116689552-116855698	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11197000	TRUB1	Cis_1M	lymphoblastoid	RTeQTL
rs11197000	TECTB	cis	cerebellum	SCAN
rs11197000	TRUB1	cis	parietal	SCAN
rs11197000	ADRB1	cis	parietal	SCAN
rs11197000	TRUB1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:116698600-116702400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr10:116698800-116702400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr10:116698800-116702600	Weak transcription	Lung	lung
4	chr10:116698800-116702800	Weak transcription	Gastric	stomach
5	chr10:116698800-116702800	Weak transcription	Pancreas	Pancrea
6	chr10:116698800-116703200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr10:116698800-116730400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr10:116698800-116763600	Weak transcription	Esophagus	oesophagus
9	chr10:116699000-116705000	Weak transcription	Colonic Mucosa	Colon
10	chr10:116699000-116706400	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr10:116699200-116702200	Weak transcription	Primary monocytes fromperipheralblood	blood
12	chr10:116699200-116702400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr10:116699200-116702400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr10:116699200-116702400	Weak transcription	Left Ventricle	heart
15	chr10:116699200-116702400	Weak transcription	Right Ventricle	heart
16	chr10:116699200-116702400	Weak transcription	Small Intestine	intestine
17	chr10:116699200-116702400	Weak transcription	Thymus	Thymus
18	chr10:116699200-116702400	Weak transcription	Spleen	Spleen
19	chr10:116699200-116704800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr10:116699200-116705200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr10:116699200-116722400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr10:116699200-116722600	Weak transcription	Aorta	Aorta
23	chr10:116699400-116702000	Weak transcription	Liver	Liver
24	chr10:116699400-116702200	Weak transcription	Brain Substantia Nigra	brain
25	chr10:116699400-116702200	Weak transcription	HSMM	muscle
26	chr10:116699400-116702400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr10:116699400-116702400	Weak transcription	HSMMtube	muscle
28	chr10:116699400-116702600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr10:116699400-116704200	Weak transcription	Stomach Mucosa	stomach
30	chr10:116699400-116708000	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr10:116699600-116702000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr10:116699600-116702200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr10:116699600-116702200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr10:116699600-116702200	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr10:116699600-116702200	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr10:116699600-116702400	Weak transcription	Adipose Nuclei	Adipose
37	chr10:116699600-116702400	Weak transcription	Brain Angular Gyrus	brain
38	chr10:116699600-116702400	Weak transcription	Brain Cingulate Gyrus	brain
39	chr10:116699600-116702400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr10:116699600-116702400	Weak transcription	Fetal Lung	lung
41	chr10:116699600-116702400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr10:116699600-116702400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr10:116699600-116702600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
44	chr10:116699600-116702600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr10:116699600-116736400	Weak transcription	NHLF	lung
46	chr10:116699800-116701800	Weak transcription	Primary B cells from cord blood	blood
47	chr10:116699800-116701800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr10:116699800-116701800	Weak transcription	Osteobl	bone
49	chr10:116699800-116702000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr10:116699800-116702200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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