Variant report

Variant	rs6729468
Chromosome Location	chr2:73765253-73765254
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 124 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:120)

rs_ID	r²[population]
rs10165862	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs10189578	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10190002	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1052161	1.00[CEU][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs1083919	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1083921	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1083922	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1083923	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10865398	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11126399	0.91[CHB][hapmap]
rs11126402	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11685372	0.91[ASN][1000 genomes]
rs11688718	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11689767	0.89[ASN][1000 genomes]
rs12233112	0.87[YRI][hapmap]
rs1246094	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12465867	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs12618600	0.96[CEU][hapmap];0.82[CHB][hapmap];0.93[JPT][hapmap]
rs12620018	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap]
rs12991161	1.00[CEU][hapmap]
rs12992607	0.93[YRI][hapmap]
rs12995433	0.86[EUR][1000 genomes]
rs12996463	0.87[EUR][1000 genomes]
rs13003035	0.93[YRI][hapmap]
rs13008860	0.80[EUR][1000 genomes]
rs13009035	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13017182	1.00[CEU][hapmap];0.82[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap]
rs13027816	1.00[CEU][hapmap]
rs1320374	1.00[CEU][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes]
rs13386124	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13399087	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1403412	0.91[CHB][hapmap]
rs1406105	0.82[CHB][hapmap]
rs1528169	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1852647	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs1881246	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1881247	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs2017116	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs2037814	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs2091503	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2091504	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2178154	0.89[EUR][1000 genomes]
rs2421489	0.82[CHB][hapmap]
rs2421545	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes]
rs2421546	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[EUR][1000 genomes]
rs2421548	0.86[EUR][1000 genomes]
rs2421574	0.92[CEU][hapmap]
rs2421581	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2421582	0.95[CEU][hapmap];0.91[CHB][hapmap]
rs2421583	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs2421586	1.00[CEU][hapmap]
rs2421667	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2421668	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs2421669	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs2948441	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs3820700	0.91[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs4346412	0.85[EUR][1000 genomes]
rs4511748	0.82[CHB][hapmap]
rs4852305	0.82[JPT][hapmap]
rs4852306	0.88[EUR][1000 genomes]
rs4852308	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4852927	0.85[EUR][1000 genomes]
rs4852951	1.00[CEU][hapmap]
rs4852954	0.92[CEU][hapmap]
rs4852959	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[YRI][hapmap]
rs4852975	0.81[YRI][hapmap]
rs4852976	0.93[YRI][hapmap]
rs55677218	0.91[ASN][1000 genomes]
rs56054150	0.85[ASN][1000 genomes]
rs56068325	0.87[ASN][1000 genomes]
rs56770679	0.81[ASN][1000 genomes]
rs62153184	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6546826	0.91[CHB][hapmap]
rs6546827	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs6546829	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs6546832	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs6546842	0.84[ASN][1000 genomes]
rs6546846	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6546870	0.82[CHB][hapmap]
rs66931335	0.90[ASN][1000 genomes]
rs6706235	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs6706409	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs6710659	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs6722867	0.89[EUR][1000 genomes]
rs6730785	0.86[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs6732440	0.96[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6742619	0.92[CEU][hapmap];0.82[CHB][hapmap];0.88[JPT][hapmap]
rs6743576	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6744697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6745560	0.96[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6746971	0.89[EUR][1000 genomes]
rs6747145	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs6748040	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs6749680	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6757996	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67877078	0.88[ASN][1000 genomes]
rs67898050	0.84[ASN][1000 genomes]
rs68154245	0.85[ASN][1000 genomes]
rs72811939	0.93[ASN][1000 genomes]
rs7562047	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7566315	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7570683	1.00[CEU][hapmap]
rs7574291	0.91[CHB][hapmap]
rs7576824	0.91[CHB][hapmap];0.81[JPT][hapmap]
rs7585119	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7598660	0.87[CEU][hapmap]
rs7598901	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7606483	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7606947	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs7608308	0.88[ASN][1000 genomes]
rs7609249	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs780388	0.81[ASN][1000 genomes]
rs780389	0.81[ASN][1000 genomes]
rs780390	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs780391	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs780393	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs780394	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs780395	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs780396	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs802113	0.81[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
rs6729468	TPRKB	Cis_1M	lymphoblastoid	RTeQTL
rs6729468	ALMS1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73731800-73807600	Weak transcription	Hela-S3	cervix
2	chr2:73741000-73767400	Weak transcription	Rectal Smooth Muscle	rectum
3	chr2:73744200-73799800	Weak transcription	NH-A	brain
4	chr2:73747800-73786800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:73756000-73766800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:73758000-73799800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr2:73758200-73766000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:73758200-73785800	Weak transcription	Brain Substantia Nigra	brain
9	chr2:73758200-73800200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr2:73758400-73786800	Weak transcription	Brain Angular Gyrus	brain
11	chr2:73759400-73774200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:73759600-73828000	Weak transcription	Pancreas	Pancrea
13	chr2:73759800-73766200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr2:73760000-73765600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr2:73760400-73765800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:73760400-73767800	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr2:73760400-73769200	Weak transcription	Gastric	stomach
18	chr2:73760600-73828000	Weak transcription	Right Ventricle	heart
19	chr2:73760800-73787000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr2:73761000-73767000	Weak transcription	Psoas Muscle	Psoas
21	chr2:73761800-73765800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr2:73761800-73766400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr2:73762000-73765400	Strong transcription	Rectal Mucosa Donor 29	rectum
24	chr2:73762000-73766400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
25	chr2:73762000-73786600	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:73762600-73765400	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:73762600-73766400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:73762600-73767000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
29	chr2:73762600-73767000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
30	chr2:73763000-73766400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:73763000-73766400	Strong transcription	Ovary	ovary
32	chr2:73763200-73765600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr2:73763200-73766000	Strong transcription	Stomach Smooth Muscle	stomach
34	chr2:73763200-73767000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
35	chr2:73763400-73767000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:73763600-73766400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
37	chr2:73763600-73766400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr2:73763800-73765600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
39	chr2:73763800-73765800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:73763800-73766000	Strong transcription	Duodenum Mucosa	Duodenum
41	chr2:73763800-73766200	ZNF genes & repeats	Fetal Muscle Leg	muscle
42	chr2:73763800-73767000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:73763800-73785200	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr2:73764000-73765600	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
45	chr2:73764000-73765800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:73764000-73766000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
47	chr2:73764000-73766400	ZNF genes & repeats	Fetal Brain Female	brain
48	chr2:73764200-73765600	Strong transcription	Primary T cells from cord blood	blood
49	chr2:73764200-73765800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
50	chr2:73764200-73765800	ZNF genes & repeats	Dnd41	blood

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