Variant report

Variant	rs7606483
Chromosome Location	chr2:73735674-73735675
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10189578	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10190002	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1052161	0.83[EUR][1000 genomes]
rs1083919	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1083921	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1083922	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1083923	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10865398	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1091568	0.81[ASN][1000 genomes]
rs11126402	0.92[EUR][1000 genomes]
rs11685372	0.82[ASN][1000 genomes]
rs11688718	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1246094	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12995433	0.86[EUR][1000 genomes]
rs12996463	0.87[EUR][1000 genomes]
rs13009035	0.85[EUR][1000 genomes]
rs1320374	0.83[EUR][1000 genomes]
rs13386124	0.93[EUR][1000 genomes]
rs13399087	0.92[EUR][1000 genomes]
rs1528169	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1881246	0.92[EUR][1000 genomes]
rs2017116	0.82[ASN][1000 genomes]
rs2091503	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2091504	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2178154	0.90[EUR][1000 genomes]
rs2421545	0.85[EUR][1000 genomes]
rs2421546	0.89[EUR][1000 genomes]
rs2421548	0.87[EUR][1000 genomes]
rs2421667	0.81[EUR][1000 genomes]
rs3820700	0.82[ASN][1000 genomes]
rs4346412	0.82[EUR][1000 genomes]
rs4852306	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4852308	0.85[EUR][1000 genomes]
rs4852927	0.85[EUR][1000 genomes]
rs55677218	0.82[ASN][1000 genomes]
rs56770679	0.84[ASN][1000 genomes]
rs62153184	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6546842	0.88[ASN][1000 genomes]
rs6546846	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6722867	0.87[EUR][1000 genomes]
rs6729468	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6730785	0.90[EUR][1000 genomes]
rs6732440	0.82[EUR][1000 genomes]
rs6743576	0.87[EUR][1000 genomes]
rs6744697	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6745560	0.85[EUR][1000 genomes]
rs6746971	0.90[EUR][1000 genomes]
rs6749680	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6757996	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67898050	0.88[ASN][1000 genomes]
rs68154245	0.87[ASN][1000 genomes]
rs7562047	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7566315	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7585119	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7598660	0.81[EUR][1000 genomes]
rs7598901	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7609249	0.87[EUR][1000 genomes]
rs780388	0.82[ASN][1000 genomes]
rs780389	0.82[ASN][1000 genomes]
rs780390	0.81[ASN][1000 genomes]
rs780391	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs780393	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs780394	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs780395	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs802113	0.82[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	nsv428051	chr2:73717032-74030067	ZNF genes & repeats Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	esv2757806	chr2:73717032-74078592	Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	esv2759060	chr2:73717032-74078592	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv874267	chr2:73717656-73857002	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7606483	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs7606483	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73711800-73740400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr2:73713200-73757400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:73715600-73740200	Weak transcription	Esophagus	oesophagus
4	chr2:73715600-73751800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr2:73715800-73740200	Weak transcription	Gastric	stomach
6	chr2:73717400-73757800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:73718000-73740800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr2:73718000-73746800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:73718200-73740400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:73718400-73738400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:73718400-73740200	Weak transcription	Duodenum Mucosa	Duodenum
12	chr2:73718600-73740200	Weak transcription	Fetal Kidney	kidney
13	chr2:73718600-73740400	Weak transcription	Thymus	Thymus
14	chr2:73718800-73740200	Weak transcription	Aorta	Aorta
15	chr2:73718800-73740200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr2:73718800-73740400	Weak transcription	HSMMtube	muscle
17	chr2:73719000-73740200	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr2:73719000-73740400	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:73719200-73739800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:73719200-73740200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr2:73719400-73740400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr2:73719400-73747000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:73719600-73738200	Weak transcription	Primary T cells from cord blood	blood
24	chr2:73719800-73740200	Weak transcription	Primary B cells from cord blood	blood
25	chr2:73728200-73747000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:73731600-73740200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:73731600-73740200	Weak transcription	HSMM	muscle
28	chr2:73731600-73759000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr2:73731800-73739800	Weak transcription	Dnd41	blood
30	chr2:73731800-73740200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr2:73731800-73746800	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr2:73731800-73752000	Weak transcription	Fetal Heart	heart
33	chr2:73731800-73807600	Weak transcription	Hela-S3	cervix
34	chr2:73732000-73740200	Weak transcription	Fetal Lung	lung
35	chr2:73732200-73740800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:73735400-73737600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr2:73735400-73740400	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:73735600-73743000	Weak transcription	Fetal Intestine Large	intestine

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