Variant report

Variant	rs4549145
Chromosome Location	chr2:48702182-48702183
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10209255	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11125173	0.87[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11683639	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs11689622	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs13401749	1.00[ASW][hapmap];1.00[YRI][hapmap]
rs4073573	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4131784	0.87[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs59356309	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72822226	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72822230	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
3	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
4	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4549145	PPP1R21	cis	Thyroid	GTEx
rs4549145	MSH6	cis	parietal	SCAN
rs4549145	FOXN2	cis	parietal	SCAN
rs4549145	CCDC128	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48673200-48724000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:48680000-48706200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:48682600-48716200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:48687600-48707200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:48689200-48702600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr2:48689200-48735600	Strong transcription	Primary neutrophils fromperipheralblood	blood
7	chr2:48689800-48702200	Strong transcription	Primary B cells from peripheral blood	blood
8	chr2:48690000-48735600	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr2:48694000-48729400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:48694200-48753000	Weak transcription	Psoas Muscle	Psoas
11	chr2:48694400-48706600	Weak transcription	Fetal Brain Male	brain
12	chr2:48694800-48706000	Weak transcription	Small Intestine	intestine
13	chr2:48695000-48707600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr2:48695200-48706000	Weak transcription	Stomach Mucosa	stomach
15	chr2:48695200-48707200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:48695200-48707400	Weak transcription	Spleen	Spleen
17	chr2:48695200-48709800	Weak transcription	NHLF	lung
18	chr2:48695200-48723800	Weak transcription	Gastric	stomach
19	chr2:48695200-48725800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:48695200-48728000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:48695400-48706400	Weak transcription	HepG2	liver
22	chr2:48695400-48706800	Weak transcription	Brain Germinal Matrix	brain
23	chr2:48695400-48706800	Weak transcription	HMEC	breast
24	chr2:48695400-48707000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:48695400-48709200	Weak transcription	HUVEC	blood vessel
26	chr2:48695400-48728000	Weak transcription	Hela-S3	cervix
27	chr2:48695600-48713400	Weak transcription	Colonic Mucosa	Colon
28	chr2:48695600-48735200	Weak transcription	K562	blood
29	chr2:48696200-48703200	Weak transcription	Brain Anterior Caudate	brain
30	chr2:48696200-48704600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:48696200-48704600	Weak transcription	Adipose Nuclei	Adipose
32	chr2:48696200-48704600	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr2:48696200-48705200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:48696200-48706800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr2:48696200-48707200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:48696200-48721000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr2:48696400-48703800	Weak transcription	Brain Angular Gyrus	brain
38	chr2:48696400-48704200	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr2:48696400-48704400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:48696400-48704400	Weak transcription	Rectal Mucosa Donor 31	rectum
41	chr2:48696400-48704800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:48696400-48705000	Weak transcription	Esophagus	oesophagus
43	chr2:48696400-48705200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:48696400-48705200	Weak transcription	Fetal Brain Female	brain
45	chr2:48696400-48707000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:48696400-48708000	Weak transcription	Pancreas	Pancrea
47	chr2:48696400-48710000	Weak transcription	Lung	lung
48	chr2:48696400-48716400	Weak transcription	Right Ventricle	heart
49	chr2:48696400-48721600	Weak transcription	Left Ventricle	heart
50	chr2:48696400-48723800	Weak transcription	Aorta	Aorta

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