Variant report

Variant	rs55757090
Chromosome Location	chr2:48671766-48671767
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFYB	chr2:48671739-48671946	GM12878	blood:	n/a	n/a
2	WRNIP1	chr2:48671628-48671836	GM12878	blood:	n/a	n/a
3	ZNF263	chr2:48670410-48671963	HEK293-T-REx	kidney:	n/a	n/a
4	FOXA1	chr2:48671471-48672353	HepG2	liver:	n/a	n/a
5	POLR2A	chr2:48671711-48671852	MCF10A-Er-Src	breast:	n/a	n/a
6	EBF1	chr2:48671625-48671847	GM12878	blood:	n/a	n/a
7	POLR2A	chr2:48667222-48671944	GM12891	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:48671387..48674060-chr2:48675787..48677578,2	K562	blood:
2	chr2:48339056..48340844-chr2:48670929..48673082,2	K562	blood:
3	chr2:48671546..48674285-chr2:48724778..48726392,2	MCF-7	breast:
4	chr2:48670330..48672555-chr2:48677413..48681489,3	MCF-7	breast:
5	chr2:48671508..48673147-chr2:48678922..48681250,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000272663	TF binding region

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10211336	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10454133	0.91[ASN][1000 genomes]
rs10454134	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11680719	0.94[ASN][1000 genomes]
rs11683639	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11683708	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11689622	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13399936	0.93[ASN][1000 genomes]
rs13400909	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13401749	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13401752	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35913553	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4274640	0.93[ASN][1000 genomes]
rs4316980	0.91[ASN][1000 genomes]
rs4438532	0.89[ASN][1000 genomes]
rs4494796	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4547570	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4606978	0.89[ASN][1000 genomes]
rs4638844	0.87[ASN][1000 genomes]
rs55640438	0.89[ASN][1000 genomes]
rs55971719	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56156294	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56365822	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58020097	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58969359	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59045263	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs60042255	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs60825643	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60988618	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62137041	0.89[ASN][1000 genomes]
rs6732196	0.86[ASN][1000 genomes]
rs6747441	0.93[EUR][1000 genomes]
rs6749773	0.80[ASN][1000 genomes]
rs72820454	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72820474	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72820479	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72820484	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72820492	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72820494	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72820499	0.95[ASN][1000 genomes]
rs7565792	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv581775	chr2:48619869-48714938	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs55757090	PPP1R21	cis	Thyroid	GTEx
rs55757090	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48668600-48682000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:48668800-48672200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:48668800-48672600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:48668800-48672600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr2:48668800-48672600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:48668800-48672600	Weak transcription	Esophagus	oesophagus
7	chr2:48668800-48672800	Weak transcription	Left Ventricle	heart
8	chr2:48668800-48673000	Enhancers	Primary B cells from peripheral blood	blood
9	chr2:48668800-48673600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr2:48668800-48674200	Weak transcription	Small Intestine	intestine
11	chr2:48668800-48675200	Weak transcription	HSMM	muscle
12	chr2:48668800-48675800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:48668800-48675800	Weak transcription	Psoas Muscle	Psoas
14	chr2:48668800-48678800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:48668800-48679600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:48668800-48682400	Weak transcription	Lung	lung
17	chr2:48669000-48672600	Weak transcription	Placenta	Placenta
18	chr2:48669000-48672600	Weak transcription	Right Atrium	heart
19	chr2:48669000-48672800	Enhancers	Liver	Liver
20	chr2:48669000-48673200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr2:48669000-48673200	Flanking Active TSS	GM12878-XiMat	blood
22	chr2:48669000-48673600	Enhancers	Brain Substantia Nigra	brain
23	chr2:48669000-48675200	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr2:48669000-48678400	Weak transcription	Colonic Mucosa	Colon
25	chr2:48669000-48678800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr2:48669000-48679000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:48669000-48680000	Weak transcription	Fetal Stomach	stomach
28	chr2:48669000-48681800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:48669000-48683400	Weak transcription	Right Ventricle	heart
30	chr2:48669200-48671800	Enhancers	K562	blood
31	chr2:48669200-48673600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr2:48669200-48673600	Enhancers	HepG2	liver
33	chr2:48669200-48674400	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr2:48669200-48675600	Weak transcription	Adipose Nuclei	Adipose
35	chr2:48669200-48678400	Weak transcription	HUVEC	blood vessel
36	chr2:48669200-48698200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr2:48669400-48671800	Enhancers	Brain Angular Gyrus	brain
38	chr2:48669400-48672200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:48669400-48672400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:48669400-48672400	Weak transcription	NHEK	skin
41	chr2:48669400-48672600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:48669400-48672600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:48669400-48672600	Weak transcription	HMEC	breast
44	chr2:48669400-48673400	Enhancers	Brain Cingulate Gyrus	brain
45	chr2:48669400-48673600	Enhancers	Brain Inferior Temporal Lobe	brain
46	chr2:48669400-48674200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr2:48669400-48674200	Weak transcription	Fetal Thymus	thymus
48	chr2:48669400-48674400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr2:48669400-48674400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:48669400-48674600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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