Variant report

Variant	rs17362588
Chromosome Location	chr2:179721046-179721047
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 9 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs4894055	0.81[CEU][hapmap];0.88[MEX][hapmap]
rs4894057	0.88[MEX][hapmap]
rs55844607	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6433738	0.81[CEU][hapmap]
rs6734390	0.81[CEU][hapmap]
rs68003004	1.00[AFR][1000 genomes];0.82[AMR][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	nsv834470	chr2:179555152-179728726	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv934108	chr2:179556852-179729925	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv949133	chr2:179711376-180124327	Flanking Active TSS ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Heart rate	23583979	GWAS catalog

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17362588	PPP1R1C	cis	parietal	SCAN
rs17362588	FKBP7	cis	parietal	SCAN
rs17362588	CCDC141	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:179693400-179726000	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:179695800-179738400	Weak transcription	Fetal Intestine Large	intestine
3	chr2:179696400-179728800	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr2:179702200-179749200	Weak transcription	Thymus	Thymus
5	chr2:179702400-179729200	Weak transcription	Lung	lung
6	chr2:179702400-179730000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr2:179702800-179728600	Weak transcription	Pancreas	Pancrea
8	chr2:179708000-179727800	Weak transcription	Psoas Muscle	Psoas
9	chr2:179710800-179722400	Weak transcription	Fetal Lung	lung
10	chr2:179710800-179724000	Weak transcription	Fetal Intestine Small	intestine
11	chr2:179710800-179782800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:179711600-179723800	Weak transcription	Rectal Smooth Muscle	rectum
13	chr2:179711600-179728000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr2:179711600-179728400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr2:179712000-179727000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr2:179712200-179725800	Weak transcription	Left Ventricle	heart
17	chr2:179713000-179721400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:179713000-179724400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:179713400-179722800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr2:179713400-179729200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr2:179713400-179778600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:179714000-179723800	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:179717000-179790600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr2:179718200-179728600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr2:179718200-179728800	Weak transcription	Primary B cells from cord blood	blood
26	chr2:179718400-179728400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr2:179719800-179723600	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr2:179719800-179725400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:179720200-179723600	Weak transcription	NHDF-Ad	bronchial
30	chr2:179720200-179723800	Weak transcription	HSMM	muscle
31	chr2:179720200-179728000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:179720800-179721200	Enhancers	Fetal Heart	heart
33	chr2:179720800-179722200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr2:179720800-179723600	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:179720800-179723600	Weak transcription	HSMMtube	muscle
36	chr2:179720800-179726400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:179721000-179727800	Weak transcription	Primary T cells from cord blood	blood

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