Variant report

Variant	rs2177488
Chromosome Location	chr2:48761437-48761438
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:48761161..48764089-chr2:48767205..48768713,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-STON1-1	chr2:48761057-48761602	NONHSAT070624

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10184783	0.82[ASN][1000 genomes]
rs12616834	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12618125	0.85[EUR][1000 genomes]
rs13410391	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2177487	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34461314	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4528813	0.86[EUR][1000 genomes]
rs4641991	0.86[EUR][1000 genomes]
rs4953587	0.86[EUR][1000 genomes]
rs6545047	0.88[EUR][1000 genomes]
rs6754946	0.88[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
rs2177488	PPP1R21	cis	Thyroid	GTEx
rs2177488	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48758000-48766000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:48758600-48762000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:48758600-48762200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:48758800-48761800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr2:48758800-48762000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:48758800-48769000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:48758800-48772400	Weak transcription	Fetal Muscle Trunk	muscle
8	chr2:48759000-48761600	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:48759000-48761800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:48759000-48762000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr2:48759000-48765200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:48759000-48765400	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr2:48759000-48772600	Weak transcription	Fetal Muscle Leg	muscle
14	chr2:48759000-48775200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:48759000-48787000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr2:48759000-48787400	Weak transcription	Psoas Muscle	Psoas
17	chr2:48759000-48827600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:48759200-48766000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:48759200-48767000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:48759200-48793200	Weak transcription	Fetal Lung	lung
21	chr2:48759400-48762600	Weak transcription	Fetal Intestine Large	intestine
22	chr2:48759400-48767000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:48759400-48775200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:48760000-48761800	Weak transcription	Fetal Stomach	stomach
25	chr2:48760000-48766200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:48760000-48770800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:48760000-48771000	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr2:48760000-48772000	Weak transcription	Lung	lung
29	chr2:48760000-48772400	Weak transcription	Right Atrium	heart
30	chr2:48760200-48761600	Weak transcription	Placenta	Placenta
31	chr2:48760200-48761800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:48760200-48761800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:48760200-48762000	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:48760200-48762200	Weak transcription	Spleen	Spleen
35	chr2:48760200-48762400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr2:48760200-48764800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:48760200-48767000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr2:48760200-48767000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:48760400-48767400	Weak transcription	Ovary	ovary
40	chr2:48760400-48772800	Weak transcription	Left Ventricle	heart

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