Variant report

Variant	rs55676974
Chromosome Location	chr3:52328024-52328025
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	chr3:52309930..52312660-chr3:52325068..52328067,2	K562	blood:
2	chr11:64544225..64546734-chr3:52326528..52328188,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164091	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000168066	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10460962	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461027	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10461028	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10865971	0.83[EUR][1000 genomes]
rs11706515	0.94[EUR][1000 genomes]
rs11706541	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11707056	1.00[EUR][1000 genomes]
rs11708581	0.94[EUR][1000 genomes]
rs11708811	1.00[EUR][1000 genomes]
rs11710014	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11711914	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11711974	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11713464	0.81[AMR][1000 genomes]
rs11713914	0.94[EUR][1000 genomes]
rs11714358	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11715208	1.00[EUR][1000 genomes]
rs11715382	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11715391	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11717028	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11718125	0.81[AFR][1000 genomes]
rs11718729	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11719760	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11720365	0.94[EUR][1000 genomes]
rs11721277	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17052051	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17052052	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17052053	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17052054	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17263770	0.81[EUR][1000 genomes]
rs1767	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1769	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35976326	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3733063	0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3886875	0.88[EUR][1000 genomes]
rs4082828	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55806905	0.94[EUR][1000 genomes]
rs55813842	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs55847657	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56002041	0.94[EUR][1000 genomes]
rs56322342	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56352611	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56899118	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57849650	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs58531656	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58879205	0.81[AMR][1000 genomes]
rs60382084	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61644644	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6445385	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6776759	0.81[EUR][1000 genomes]
rs6783652	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6793317	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6809248	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs724801	0.82[EUR][1000 genomes]
rs729555	0.82[EUR][1000 genomes]
rs73072990	0.88[EUR][1000 genomes]
rs73088773	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73088783	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088785	0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73088791	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73088800	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73091166	0.94[EUR][1000 genomes]
rs73091168	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs746239	0.94[EUR][1000 genomes]
rs7615405	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7628461	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7633687	0.94[EUR][1000 genomes]
rs7638204	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7643913	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
3	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
4	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
5	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
6	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
7	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
8	nsv984542	chr3:52285682-52516115	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	94 gene(s)	inside rSNPs	diseases
9	nsv834696	chr3:52317478-52479537	Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	45 gene(s)	inside rSNPs	diseases
10	esv3402579	chr3:52323712-52330410	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs55676974	PPM1M	cis	Artery Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52322600-52331800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:52322600-52332000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:52322600-52334400	Weak transcription	NHDF-Ad	bronchial
4	chr3:52322800-52330800	Weak transcription	Brain Germinal Matrix	brain
5	chr3:52322800-52331400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:52322800-52331400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:52322800-52331600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:52322800-52331800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:52323000-52328200	Weak transcription	Psoas Muscle	Psoas
10	chr3:52323000-52332600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:52323200-52341000	Weak transcription	Small Intestine	intestine
12	chr3:52323400-52333200	Weak transcription	HUVEC	blood vessel
13	chr3:52323600-52328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:52323600-52330400	Weak transcription	HSMM	muscle
15	chr3:52323800-52329800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr3:52324000-52331800	Weak transcription	K562	blood
17	chr3:52324000-52332800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr3:52324200-52328200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:52324200-52331400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr3:52324400-52328800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:52324400-52328800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:52324400-52329600	Strong transcription	Thymus	Thymus
23	chr3:52324400-52330200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:52324400-52331000	Strong transcription	Primary T cells from cord blood	blood
25	chr3:52324400-52332000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:52324600-52328200	Strong transcription	Brain Inferior Temporal Lobe	brain
27	chr3:52324600-52329000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr3:52324600-52329200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:52324600-52329400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr3:52324600-52329600	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr3:52324600-52329600	Strong transcription	Fetal Muscle Leg	muscle
32	chr3:52324600-52330200	Strong transcription	Placenta	Placenta
33	chr3:52324600-52330400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr3:52324600-52330600	Strong transcription	Monocytes-CD14+_RO01746	blood
35	chr3:52324800-52328200	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr3:52324800-52328200	Strong transcription	NHLF	lung
37	chr3:52324800-52328400	Strong transcription	Fetal Muscle Trunk	muscle
38	chr3:52324800-52329000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:52324800-52329200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr3:52324800-52329200	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr3:52325000-52328200	Strong transcription	Brain Angular Gyrus	brain
42	chr3:52325000-52328800	Strong transcription	Brain Substantia Nigra	brain
43	chr3:52325000-52328800	Strong transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:52325000-52329200	Strong transcription	Primary B cells from cord blood	blood
45	chr3:52325000-52330200	Strong transcription	Brain Cingulate Gyrus	brain
46	chr3:52325000-52331200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr3:52325000-52332000	Strong transcription	Right Ventricle	heart
48	chr3:52325200-52328400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr3:52325200-52328800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:52325200-52330800	Strong transcription	Spleen	Spleen

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