Variant report

Variant	rs11050170
Chromosome Location	chr12:29430146-29430147
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10047562	0.83[ASN][1000 genomes]
rs1035604	0.90[ASN][1000 genomes]
rs10771507	0.82[ASN][1000 genomes]
rs10771508	0.84[ASN][1000 genomes]
rs10843366	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10843367	0.96[ASN][1000 genomes]
rs10843371	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10843373	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10843375	0.80[EUR][1000 genomes]
rs10843377	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843382	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843384	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10843403	0.82[ASN][1000 genomes]
rs11050152	0.92[ASN][1000 genomes]
rs11050157	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11050161	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11050162	0.88[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs11050163	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11050167	0.98[ASN][1000 genomes]
rs11050173	0.87[ASN][1000 genomes]
rs11050181	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11050187	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11050188	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11050189	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11050191	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11050192	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11050193	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11050194	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11050208	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11833737	0.81[EUR][1000 genomes]
rs12228468	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12231498	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12366505	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12366527	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16934135	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1989478	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1991114	0.90[ASN][1000 genomes]
rs2042511	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2194518	0.97[ASN][1000 genomes]
rs2194519	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2194520	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2216853	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2216854	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3764953	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3782506	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3782509	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3782511	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4331146	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57803026	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6487796	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6487801	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6487804	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6487805	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6487808	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67146951	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67517901	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7131987	0.83[ASN][1000 genomes]
rs7139273	0.85[EUR][1000 genomes]
rs7294598	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7299861	0.81[ASN][1000 genomes]
rs7301188	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7302129	0.98[ASN][1000 genomes]
rs7308125	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7311912	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7312164	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7316004	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs737160	0.84[EUR][1000 genomes]
rs7954278	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7954871	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7957339	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7973786	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7976961	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs962866	0.85[EUR][1000 genomes]
rs9738721	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][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	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	40 gene(s)	inside rSNPs	diseases
4	esv3372345	chr12:29425485-29430283	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11050170	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29414400-29434000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:29417200-29465400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:29419200-29430600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr12:29419800-29430400	Weak transcription	Brain Angular Gyrus	brain
5	chr12:29420400-29435000	Weak transcription	HUVEC	blood vessel
6	chr12:29420600-29431600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:29421000-29432000	Weak transcription	Adipose Nuclei	Adipose
8	chr12:29422000-29455600	Weak transcription	Left Ventricle	heart
9	chr12:29422000-29465000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr12:29422200-29430400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:29422200-29434800	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr12:29422400-29434400	Weak transcription	Fetal Kidney	kidney
13	chr12:29424600-29435200	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:29424800-29433400	Weak transcription	Primary hematopoietic stem cells	blood
15	chr12:29424800-29434800	Weak transcription	Dnd41	blood
16	chr12:29425000-29434400	Weak transcription	Fetal Stomach	stomach
17	chr12:29425200-29435600	Weak transcription	Brain Hippocampus Middle	brain
18	chr12:29426200-29430600	Weak transcription	Fetal Intestine Large	intestine
19	chr12:29426200-29430800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr12:29426600-29430200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr12:29426600-29431400	Weak transcription	Fetal Muscle Leg	muscle
22	chr12:29426600-29434400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr12:29426600-29440600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:29426800-29430400	Weak transcription	Fetal Intestine Small	intestine
25	chr12:29426800-29432200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr12:29426800-29433600	Weak transcription	Fetal Muscle Trunk	muscle
27	chr12:29426800-29436200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr12:29426800-29440600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:29426800-29472800	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:29427000-29431200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:29427000-29433600	Weak transcription	Spleen	Spleen
32	chr12:29427000-29435200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr12:29427000-29452200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
35	chr12:29427800-29432000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr12:29427800-29438400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:29428000-29430200	Weak transcription	NH-A	brain
38	chr12:29428600-29434200	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr12:29429000-29432000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:29429000-29433400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr12:29429000-29460200	Weak transcription	Primary T cells from cord blood	blood
42	chr12:29429200-29463600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr12:29429400-29430200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:29429400-29460400	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr12:29429800-29430200	Weak transcription	Osteobl	bone

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