Variant report

Variant	rs12152435
Chromosome Location	chr3:160228727-160228728
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10923	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10936201	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10936203	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11708118	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11709232	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11711627	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11712392	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11713230	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11716413	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11719750	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11720689	0.82[EUR][1000 genomes]
rs11721112	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12630564	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12630770	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12630956	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12638633	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639488	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13065269	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13074231	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16831207	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17236494	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17826137	0.82[EUR][1000 genomes]
rs17826173	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17826257	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1873076	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1920663	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1971128	0.81[AFR][1000 genomes]
rs2095529	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2099496	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2123003	0.81[AFR][1000 genomes]
rs2141668	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2178451	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35008770	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3732706	0.81[AFR][1000 genomes]
rs3773369	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4679886	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4679892	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4679903	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4679904	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4680581	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4680586	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56952700	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60395700	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6441311	0.82[EUR][1000 genomes]
rs73875259	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73875285	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73875290	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7644186	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[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	nsv532666	chr3:159777847-160703202	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv1000453	chr3:159853305-160366357	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
3	nsv536779	chr3:159853305-160366357	Strong transcription Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	259 gene(s)	inside rSNPs	diseases
4	esv1800136	chr3:159950498-160278160	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
5	esv1801767	chr3:159950498-160279411	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
6	nsv1008519	chr3:160038710-160292589	Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
7	esv1801686	chr3:160089896-160248363	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	211 gene(s)	inside rSNPs	diseases
8	esv1797113	chr3:160217483-160245980	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv877700	chr3:160223172-160248363	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv877701	chr3:160228001-160283815	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12152435	SMC4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160204000-160238200	Weak transcription	Small Intestine	intestine
2	chr3:160215600-160254200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr3:160215800-160254000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:160215800-160254200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:160215800-160254200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr3:160216000-160254200	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:160216200-160249200	Strong transcription	Liver	Liver
8	chr3:160216200-160254200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr3:160216400-160228800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:160216400-160254400	Strong transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:160216800-160253800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr3:160217200-160254000	Strong transcription	Dnd41	blood
13	chr3:160217400-160259600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:160217800-160235000	Weak transcription	Fetal Brain Male	brain
15	chr3:160218800-160244800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr3:160219600-160233400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:160219800-160242200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:160219800-160263600	Weak transcription	Right Ventricle	heart
19	chr3:160220600-160246200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:160220600-160261200	Weak transcription	Pancreas	Pancrea
21	chr3:160220800-160232600	Weak transcription	Aorta	Aorta
22	chr3:160221600-160249000	Strong transcription	HUVEC	blood vessel
23	chr3:160222000-160230400	Weak transcription	HSMMtube	muscle
24	chr3:160222200-160244600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr3:160223400-160243000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr3:160224400-160233200	Weak transcription	Gastric	stomach
27	chr3:160224400-160233200	Weak transcription	Lung	lung
28	chr3:160225600-160259800	Weak transcription	Stomach Mucosa	stomach
29	chr3:160225800-160230400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:160225800-160231000	Weak transcription	Thymus	Thymus
31	chr3:160225800-160231200	Weak transcription	Fetal Kidney	kidney
32	chr3:160225800-160236800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:160226000-160231000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr3:160226000-160233400	Strong transcription	Hela-S3	cervix
35	chr3:160226000-160235000	Weak transcription	Fetal Heart	heart
36	chr3:160226000-160244000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:160226200-160231400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr3:160227000-160231200	Weak transcription	Rectal Smooth Muscle	rectum
39	chr3:160227000-160232800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:160227000-160233200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr3:160227000-160234800	Weak transcription	Psoas Muscle	Psoas
42	chr3:160227200-160230000	Weak transcription	A549	lung
43	chr3:160227200-160230000	Weak transcription	GM12878-XiMat	blood
44	chr3:160227200-160230400	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:160227200-160230400	Weak transcription	Ovary	ovary
46	chr3:160227200-160230600	Weak transcription	Fetal Brain Female	brain
47	chr3:160227200-160230800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:160227200-160230800	Weak transcription	Brain Anterior Caudate	brain
49	chr3:160227200-160230800	Weak transcription	Fetal Lung	lung
50	chr3:160227200-160231000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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