Variant report

Variant	rs60335031
Chromosome Location	chr2:100060483-100060484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100055571..100061199-chr2:100104819..100108042,8	MCF-7	breast:
2	chr2:100059250..100062216-chr2:100105245..100107789,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs1000409	0.81[ASN][1000 genomes]
rs1011633	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10170425	0.81[ASN][1000 genomes]
rs10172068	0.81[ASN][1000 genomes]
rs10172752	0.81[ASN][1000 genomes]
rs1053544	0.80[AMR][1000 genomes]
rs10865031	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11899745	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12052986	0.90[AMR][1000 genomes]
rs12465846	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13392042	0.81[ASN][1000 genomes]
rs1451246	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1839666	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1839667	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1901283	0.81[ASN][1000 genomes]
rs1973011	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2053917	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2122748	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2290261	0.80[AMR][1000 genomes]
rs2309585	0.81[ASN][1000 genomes]
rs2309604	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28369943	0.81[ASN][1000 genomes]
rs28382984	0.80[AMR][1000 genomes]
rs3749087	0.82[AMR][1000 genomes]
rs3792134	0.81[ASN][1000 genomes]
rs3792137	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3792142	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792144	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3792149	0.81[ASN][1000 genomes]
rs4143760	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4476396	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4851206	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4851208	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs4851209	0.80[ASN][1000 genomes]
rs57977991	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58958283	0.80[AMR][1000 genomes]
rs60257640	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62155809	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6542879	0.81[ASN][1000 genomes]
rs6542880	0.80[ASN][1000 genomes]
rs6542881	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6711073	0.80[AMR][1000 genomes]
rs6715321	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6737560	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6761390	0.82[AMR][1000 genomes]
rs717454	0.82[AMR][1000 genomes]
rs7560996	0.82[AMR][1000 genomes]
rs7563455	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7563462	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7564587	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7567674	0.81[ASN][1000 genomes]
rs7572779	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7580448	0.80[ASN][1000 genomes]
rs7585019	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7589365	0.87[AMR][1000 genomes]
rs7593274	0.80[AMR][1000 genomes]
rs7597141	0.82[AMR][1000 genomes]
rs7598629	0.81[ASN][1000 genomes]
rs769105	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs896248	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs896249	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs959929	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv1014604	chr2:99980851-100097884	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1006625	chr2:99984550-100096371	Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
4	nsv1014161	chr2:100021040-100063406	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs60335031	LYG1	cis	Adipose Subcutaneous	GTEx
rs60335031	LYG1	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100005800-100062600	Strong transcription	Dnd41	blood
2	chr2:100005800-100066000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:100006000-100081200	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:100021200-100077800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:100032600-100078000	Weak transcription	Psoas Muscle	Psoas
6	chr2:100034200-100088800	Weak transcription	Small Intestine	intestine
7	chr2:100036800-100074800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:100038200-100063200	Weak transcription	Fetal Intestine Small	intestine
9	chr2:100038200-100073800	Weak transcription	Esophagus	oesophagus
10	chr2:100041400-100077800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:100041600-100083400	Weak transcription	Brain Substantia Nigra	brain
12	chr2:100042800-100065000	Weak transcription	Lung	lung
13	chr2:100045000-100064200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr2:100045400-100068200	Weak transcription	Ovary	ovary
15	chr2:100047800-100063200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:100048200-100090600	Weak transcription	Stomach Mucosa	stomach
17	chr2:100048400-100067800	Weak transcription	Fetal Heart	heart
18	chr2:100048600-100064000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:100048600-100068200	Weak transcription	Spleen	Spleen
20	chr2:100048800-100070400	Weak transcription	Fetal Brain Female	brain
21	chr2:100050000-100065000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr2:100051800-100064600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr2:100053800-100075800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr2:100055400-100083200	Weak transcription	Right Ventricle	heart
25	chr2:100055600-100062000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:100055600-100062200	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:100055600-100063800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr2:100055600-100064000	Weak transcription	Stomach Smooth Muscle	stomach
29	chr2:100055600-100065000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr2:100055600-100065000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:100055600-100065000	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:100055600-100065000	Weak transcription	NH-A	brain
33	chr2:100055600-100065400	Weak transcription	Brain Germinal Matrix	brain
34	chr2:100055600-100068600	Weak transcription	Rectal Smooth Muscle	rectum
35	chr2:100055600-100071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr2:100055600-100078200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr2:100055600-100079800	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:100055800-100062600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:100055800-100063200	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr2:100055800-100063800	Weak transcription	Fetal Stomach	stomach
41	chr2:100055800-100064000	Weak transcription	HMEC	breast
42	chr2:100055800-100064200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:100055800-100064200	Weak transcription	HSMMtube	muscle
44	chr2:100055800-100064200	Weak transcription	Osteobl	bone
45	chr2:100055800-100064400	Weak transcription	Colonic Mucosa	Colon
46	chr2:100055800-100065000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr2:100055800-100067800	Weak transcription	Fetal Lung	lung
48	chr2:100055800-100072200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:100055800-100072800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:100055800-100076200	Weak transcription	Aorta	Aorta

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