Variant report

Variant	rs58086269
Chromosome Location	chr2:99945794-99945795
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99936302..99938598-chr2:99944991..99946972,2	MCF-7	breast:
2	chr2:99945014..99949225-chr2:99950035..99954681,7	K562	blood:
3	chr2:99771234..99772916-chr2:99943492..99946136,2	K562	blood:
4	chr2:99905599..99909122-chr2:99945751..99948599,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158417	Chromatin interaction
ENSG00000273155	Chromatin interaction
ENSG00000115514	Chromatin interaction
ENSG00000144182	Chromatin interaction
ENSG00000135951	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs1011633	0.81[EUR][1000 genomes]
rs1053544	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10779902	0.83[ASN][1000 genomes]
rs10865031	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11123775	0.81[ASN][1000 genomes]
rs11674219	0.85[ASN][1000 genomes]
rs11687870	0.88[ASN][1000 genomes]
rs11884686	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11892441	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11899745	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12052986	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12464785	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12465846	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12475639	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12618779	0.82[ASN][1000 genomes]
rs12621141	0.82[ASN][1000 genomes]
rs13017871	0.87[ASN][1000 genomes]
rs13018274	0.81[ASN][1000 genomes]
rs13028869	0.85[ASN][1000 genomes]
rs1451246	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1584647	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1584648	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17022433	0.81[ASN][1000 genomes]
rs17022564	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17022629	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1807985	0.81[ASN][1000 genomes]
rs1839667	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1955393	0.81[ASN][1000 genomes]
rs1973011	0.80[AMR][1000 genomes]
rs2053917	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2122748	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2290255	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2290261	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2309576	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2309617	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28382946	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28382984	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3749087	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3791212	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3792137	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3792142	0.80[AMR][1000 genomes]
rs3792144	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3811555	0.86[ASN][1000 genomes]
rs4476396	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4850901	0.88[ASN][1000 genomes]
rs4851204	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4851206	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55815229	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57242893	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57977991	0.82[AMR][1000 genomes]
rs58958283	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59178618	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59661148	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59816625	0.81[ASN][1000 genomes]
rs60257640	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs61103312	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62153855	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62155809	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6708861	0.86[ASN][1000 genomes]
rs6709240	0.88[ASN][1000 genomes]
rs6711073	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6713608	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6720885	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6732750	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6734290	0.84[ASN][1000 genomes]
rs717454	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7558062	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7560996	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7563455	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7563462	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7571202	0.84[ASN][1000 genomes]
rs7572779	0.81[EUR][1000 genomes]
rs7584127	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7585019	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7589365	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7593274	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7597045	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7597141	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7602923	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7606977	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7609108	0.87[ASN][1000 genomes]
rs769105	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs896248	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs901596	0.81[ASN][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	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv874699	chr2:99898998-100010044	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv979073	chr2:99927377-99947554	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs58086269	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs58086269	LYG1	cis	Nerve Tibial	GTEx
rs58086269	LYG1	cis	Adipose Subcutaneous	GTEx
rs58086269	REV1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99917200-99948200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr2:99928200-99951800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:99932000-99951400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:99933000-99949800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:99933000-99950000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:99933400-99945800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr2:99933400-99946800	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr2:99933400-99949000	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:99933400-99949600	Strong transcription	Fetal Muscle Leg	muscle
10	chr2:99933400-99949600	Strong transcription	Skeletal Muscle Female	skeletal muscle
11	chr2:99933400-99949800	Strong transcription	Duodenum Mucosa	Duodenum
12	chr2:99933400-99950400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr2:99933400-99950600	Strong transcription	Primary neutrophils fromperipheralblood	blood
14	chr2:99933400-99950600	Strong transcription	Fetal Thymus	thymus
15	chr2:99933600-99949000	Strong transcription	Thymus	Thymus
16	chr2:99933600-99949400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr2:99933600-99949600	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr2:99933600-99949600	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr2:99933600-99949600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:99933600-99949600	Strong transcription	Liver	Liver
21	chr2:99933600-99949600	Strong transcription	Duodenum Smooth Muscle	Duodenum
22	chr2:99933600-99949800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:99933600-99949800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:99933600-99949800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:99933600-99949800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr2:99933600-99949800	Strong transcription	Adipose Nuclei	Adipose
27	chr2:99933600-99949800	Strong transcription	Fetal Muscle Trunk	muscle
28	chr2:99933600-99949800	Strong transcription	Dnd41	blood
29	chr2:99933600-99949800	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr2:99933600-99950000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr2:99933600-99950000	Strong transcription	Primary B cells from peripheral blood	blood
32	chr2:99933600-99950000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr2:99933600-99950000	Strong transcription	GM12878-XiMat	blood
34	chr2:99933600-99950200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr2:99933600-99950400	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr2:99933600-99950400	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr2:99933600-99950400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:99933600-99950400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:99933600-99950800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:99933800-99948800	Strong transcription	HepG2	liver
41	chr2:99933800-99949800	Strong transcription	Fetal Intestine Large	intestine
42	chr2:99933800-99950000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr2:99933800-99950000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr2:99933800-99950400	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr2:99933800-99950400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr2:99934000-99947200	Strong transcription	Lung	lung
47	chr2:99934000-99948800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:99934000-99949600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:99934600-99949800	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr2:99934600-99949800	Strong transcription	Placenta	Placenta

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