Variant report

Variant	rs6545039
Chromosome Location	chr2:48646493-48646494
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:48336922..48340984-chr2:48645140..48651052,10	MCF-7	breast:
2	chr2:48337553..48343006-chr2:48644200..48649231,9	MCF-7	breast:
3	chr2:48645150..48646743-chr2:48650153..48652145,2	MCF-7	breast:
4	chr2:48641901..48644739-chr2:48646186..48647771,2	K562	blood:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10186237	0.89[CEU][hapmap]
rs10199431	0.89[CEU][hapmap]
rs10208627	0.80[EUR][1000 genomes]
rs10454133	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11676168	0.89[CEU][hapmap]
rs11682044	0.81[CEU][hapmap]
rs11682931	0.86[EUR][1000 genomes]
rs11685861	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs11690690	0.88[EUR][1000 genomes]
rs12105983	0.81[EUR][1000 genomes]
rs13388291	0.88[CEU][hapmap]
rs13392004	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13429377	0.81[EUR][1000 genomes]
rs4267555	0.82[AMR][1000 genomes]
rs4274640	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4293602	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs4344965	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs4356705	0.88[ASN][1000 genomes]
rs4411759	0.89[CEU][hapmap]
rs4497915	0.85[CEU][hapmap];0.86[CHB][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4528813	0.86[CHB][hapmap]
rs4547573	0.86[CEU][hapmap]
rs4953579	0.93[JPT][hapmap]
rs4953581	0.81[AMR][1000 genomes]
rs56163539	0.81[EUR][1000 genomes]
rs62137015	0.88[EUR][1000 genomes]
rs62137019	0.85[EUR][1000 genomes]
rs62137041	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6545027	0.85[CEU][hapmap]
rs6545030	0.93[CEU][hapmap]
rs6545036	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs6712029	0.92[CEU][hapmap]
rs6735288	0.85[EUR][1000 genomes]
rs6743757	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs6749773	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7562069	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs7562816	0.87[EUR][1000 genomes]
rs7579932	0.93[CEU][hapmap];0.88[EUR][1000 genomes]
rs7600794	0.96[CEU][hapmap];0.88[EUR][1000 genomes]
rs7606104	0.96[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	nsv518718	chr2:48624007-48650308	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6545039	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48639600-48647400	Enhancers	Liver	Liver
2	chr2:48640400-48647600	Weak transcription	Colon Smooth Muscle	Colon
3	chr2:48640400-48647600	Weak transcription	Ovary	ovary
4	chr2:48640600-48647800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:48641000-48647400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:48642400-48647600	Weak transcription	Pancreas	Pancrea
7	chr2:48642800-48647400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:48642800-48647400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:48642800-48647400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:48642800-48647400	Weak transcription	NH-A	brain
11	chr2:48642800-48647600	Weak transcription	Osteobl	bone
12	chr2:48643000-48647200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr2:48643000-48647600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr2:48643000-48647600	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr2:48643000-48647600	Weak transcription	NHLF	lung
16	chr2:48643200-48647400	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:48643200-48647600	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr2:48643200-48647600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:48643200-48647800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr2:48643400-48647000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr2:48643400-48647000	Enhancers	Brain Hippocampus Middle	brain
22	chr2:48643400-48647600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr2:48643400-48647800	Weak transcription	Fetal Kidney	kidney
24	chr2:48643600-48646600	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr2:48643600-48646800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr2:48643600-48646800	Weak transcription	HMEC	breast
27	chr2:48643600-48647000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:48643600-48647000	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:48643600-48647000	Weak transcription	Placenta	Placenta
30	chr2:48643600-48647000	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr2:48643600-48647000	Weak transcription	Right Atrium	heart
32	chr2:48643600-48647000	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr2:48643600-48647200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:48643600-48647200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:48643600-48647200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr2:48643600-48647200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:48643600-48647200	Weak transcription	Right Ventricle	heart
38	chr2:48643600-48647400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr2:48643600-48647400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr2:48643600-48647400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr2:48643600-48647400	Weak transcription	Colonic Mucosa	Colon
42	chr2:48643600-48647400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr2:48643600-48647400	Weak transcription	Fetal Brain Male	brain
44	chr2:48643600-48647400	Weak transcription	Left Ventricle	heart
45	chr2:48643600-48647400	Weak transcription	Lung	lung
46	chr2:48643600-48647400	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr2:48643600-48647400	Weak transcription	A549	lung
48	chr2:48643600-48647400	Weak transcription	NHDF-Ad	bronchial
49	chr2:48643600-48647600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:48643600-48647600	Weak transcription	Primary B cells from peripheral blood	blood

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