Variant report

Variant	rs60953992
Chromosome Location	chr4:152111196-152111197
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12503016	0.85[ASN][1000 genomes]
rs12504166	0.82[ASN][1000 genomes]
rs12508270	0.97[ASN][1000 genomes]
rs12511209	0.86[ASN][1000 genomes]
rs17633530	0.86[ASN][1000 genomes]
rs17633537	0.86[ASN][1000 genomes]
rs17633600	0.82[ASN][1000 genomes]
rs36115072	0.91[ASN][1000 genomes]
rs58496896	0.86[ASN][1000 genomes]
rs60367453	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61442068	0.99[ASN][1000 genomes]
rs6858302	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7681468	0.99[ASN][1000 genomes]
rs7681571	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60953992	RPS3A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152088200-152114600	Weak transcription	Psoas Muscle	Psoas
2	chr4:152096600-152118000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:152096800-152120600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:152097200-152123600	Weak transcription	Pancreas	Pancrea
5	chr4:152097200-152136600	Weak transcription	Colonic Mucosa	Colon
6	chr4:152097400-152111600	Weak transcription	Lung	lung
7	chr4:152097400-152123600	Weak transcription	Aorta	Aorta
8	chr4:152097600-152111400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:152097600-152111600	Weak transcription	Fetal Stomach	stomach
10	chr4:152097600-152128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr4:152097800-152111400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:152097800-152117200	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:152097800-152120000	Weak transcription	Stomach Smooth Muscle	stomach
14	chr4:152098200-152111600	Weak transcription	Fetal Muscle Leg	muscle
15	chr4:152098200-152117000	Weak transcription	Brain Anterior Caudate	brain
16	chr4:152098200-152118400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr4:152098400-152111400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr4:152098400-152111400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr4:152098400-152116600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr4:152098400-152118400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr4:152098400-152147200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr4:152100200-152116600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:152100600-152118000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr4:152106200-152111400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr4:152106400-152111600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:152106400-152112200	Weak transcription	Brain Hippocampus Middle	brain
27	chr4:152106600-152112200	Weak transcription	Brain Inferior Temporal Lobe	brain
28	chr4:152106600-152115600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr4:152106600-152116600	Weak transcription	NHEK	skin
30	chr4:152106600-152117200	Weak transcription	Left Ventricle	heart
31	chr4:152106800-152111800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr4:152106800-152111800	Weak transcription	Fetal Intestine Large	intestine
33	chr4:152106800-152113800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr4:152106800-152116600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr4:152107200-152111600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr4:152107200-152111600	Weak transcription	Right Atrium	heart
37	chr4:152107200-152111600	Weak transcription	Right Ventricle	heart
38	chr4:152107200-152116000	Weak transcription	Ovary	ovary
39	chr4:152107200-152120000	Weak transcription	HepG2	liver
40	chr4:152107400-152111600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:152107600-152113400	Weak transcription	Fetal Heart	heart
42	chr4:152107600-152116600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr4:152109400-152111400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr4:152110000-152113600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr4:152110200-152113800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:152110800-152111200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr4:152110800-152111800	Enhancers	Adipose Nuclei	Adipose
48	chr4:152110800-152112600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
49	chr4:152110800-152113400	ZNF genes & repeats	Fetal Intestine Small	intestine

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