Variant report

Variant	rs12616834
Chromosome Location	chr2:48759274-48759275
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10184783	0.89[ASN][1000 genomes]
rs12618125	0.92[EUR][1000 genomes]
rs12620002	0.85[ASN][1000 genomes]
rs13410391	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2177487	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2177488	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34461314	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4296472	0.81[ASN][1000 genomes]
rs4528813	0.94[EUR][1000 genomes]
rs4641991	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4952914	0.84[EUR][1000 genomes]
rs4953587	0.94[EUR][1000 genomes]
rs6545047	0.95[EUR][1000 genomes]
rs6733533	0.94[ASN][1000 genomes]
rs6754946	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005954	chr2:48692696-48905723	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535682	chr2:48692696-48905723	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv833981	chr2:48705444-48878179	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1007491	chr2:48752185-48796441	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv535683	chr2:48752185-48796441	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12616834	PPP1R21	cis	Thyroid	GTEx
rs12616834	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48756600-48759800	Active TSS	Stomach Smooth Muscle	stomach
2	chr2:48756800-48759800	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr2:48757800-48759400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr2:48758000-48759800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:48758000-48759800	Weak transcription	Spleen	Spleen
6	chr2:48758000-48766000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr2:48758600-48762000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:48758600-48762200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:48758800-48759400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr2:48758800-48759800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr2:48758800-48760000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:48758800-48760000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:48758800-48760000	Enhancers	Right Ventricle	heart
14	chr2:48758800-48760200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr2:48758800-48760200	Enhancers	Placenta	Placenta
16	chr2:48758800-48761800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:48758800-48762000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr2:48758800-48769000	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:48758800-48772400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr2:48759000-48759400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr2:48759000-48759400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:48759000-48759400	Enhancers	HSMMtube	muscle
23	chr2:48759000-48759600	Weak transcription	Fetal Kidney	kidney
24	chr2:48759000-48759800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:48759000-48760000	Weak transcription	NHDF-Ad	bronchial
26	chr2:48759000-48760200	Enhancers	Adipose Nuclei	Adipose
27	chr2:48759000-48760200	Enhancers	HUVEC	blood vessel
28	chr2:48759000-48760400	Enhancers	Left Ventricle	heart
29	chr2:48759000-48761600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr2:48759000-48761800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr2:48759000-48762000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr2:48759000-48765200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:48759000-48765400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:48759000-48772600	Weak transcription	Fetal Muscle Leg	muscle
35	chr2:48759000-48775200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr2:48759000-48787000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr2:48759000-48787400	Weak transcription	Psoas Muscle	Psoas
38	chr2:48759000-48827600	Weak transcription	Muscle Satellite Cultured Cells	--
39	chr2:48759200-48759400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr2:48759200-48759400	Enhancers	Esophagus	oesophagus
41	chr2:48759200-48759400	Enhancers	Fetal Intestine Large	intestine
42	chr2:48759200-48759400	Flanking Active TSS	Right Atrium	heart
43	chr2:48759200-48759600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:48759200-48759600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:48759200-48759600	Weak transcription	Fetal Stomach	stomach
46	chr2:48759200-48759800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr2:48759200-48759800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:48759200-48759800	Active TSS	Rectal Smooth Muscle	rectum
49	chr2:48759200-48759800	Weak transcription	NHEK	skin
50	chr2:48759200-48759800	Weak transcription	Osteobl	bone

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