Variant report

Variant	rs62153852
Chromosome Location	chr2:99934713-99934714
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	chr2:99929266..99930984-chr2:99932298..99935090,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10496336	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11885942	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11893359	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11896520	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12466388	0.84[ASN][1000 genomes]
rs12474305	0.81[EUR][1000 genomes]
rs1922624	0.84[ASN][1000 genomes]
rs2141907	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2305352	0.86[EUR][1000 genomes]
rs2309618	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28369945	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28382977	0.86[EUR][1000 genomes]
rs3087403	0.84[EUR][1000 genomes]
rs3792143	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3792150	0.84[EUR][1000 genomes]
rs4851203	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851207	0.81[EUR][1000 genomes]
rs61436115	0.84[EUR][1000 genomes]
rs62155769	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62155807	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6714650	0.81[EUR][1000 genomes]
rs6748200	0.83[EUR][1000 genomes]
rs737094	0.83[EUR][1000 genomes]
rs73963398	0.84[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62153852	LYG1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99892400-99935000	Weak transcription	Brain Angular Gyrus	brain
2	chr2:99894200-99934800	Weak transcription	Gastric	stomach
3	chr2:99895400-99935000	Weak transcription	Pancreas	Pancrea
4	chr2:99898400-99938600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:99899800-99935000	Weak transcription	Esophagus	oesophagus
6	chr2:99901200-99936600	Weak transcription	Fetal Brain Male	brain
7	chr2:99901600-99941200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:99915000-99942800	Weak transcription	Aorta	Aorta
9	chr2:99916000-99935000	Weak transcription	Hela-S3	cervix
10	chr2:99917200-99948200	Weak transcription	Pancreatic Islets	Pancreatic Islet
11	chr2:99919000-99935000	Weak transcription	Right Ventricle	heart
12	chr2:99919200-99938600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:99919800-99935000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr2:99920200-99935000	Weak transcription	Brain Substantia Nigra	brain
15	chr2:99921000-99942000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:99921600-99939200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:99922600-99939000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr2:99928200-99951800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr2:99928600-99935000	Weak transcription	HMEC	breast
20	chr2:99928600-99935000	Weak transcription	NHEK	skin
21	chr2:99931000-99935000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr2:99931400-99935200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr2:99932000-99935000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:99932000-99951400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:99932400-99935000	Weak transcription	Fetal Heart	heart
26	chr2:99932400-99935000	Weak transcription	NHLF	lung
27	chr2:99933000-99949800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:99933000-99950000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:99933400-99935000	Weak transcription	NH-A	brain
30	chr2:99933400-99935600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:99933400-99936800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr2:99933400-99938200	Strong transcription	Primary B cells from cord blood	blood
33	chr2:99933400-99940400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:99933400-99940600	Strong transcription	Left Ventricle	heart
35	chr2:99933400-99945800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:99933400-99946800	Strong transcription	Primary T helper cells PMA-I stimulated	--
37	chr2:99933400-99949000	Strong transcription	Primary T helper cells fromperipheralblood	blood
38	chr2:99933400-99949600	Strong transcription	Fetal Muscle Leg	muscle
39	chr2:99933400-99949600	Strong transcription	Skeletal Muscle Female	skeletal muscle
40	chr2:99933400-99949800	Strong transcription	Duodenum Mucosa	Duodenum
41	chr2:99933400-99950400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:99933400-99950600	Strong transcription	Primary neutrophils fromperipheralblood	blood
43	chr2:99933400-99950600	Strong transcription	Fetal Thymus	thymus
44	chr2:99933600-99935400	Strong transcription	Sigmoid Colon	Sigmoid Colon
45	chr2:99933600-99935600	Strong transcription	Brain Germinal Matrix	brain
46	chr2:99933600-99935600	Strong transcription	Psoas Muscle	Psoas
47	chr2:99933600-99935800	Strong transcription	Brain Anterior Caudate	brain
48	chr2:99933600-99935800	Strong transcription	HSMMtube	muscle
49	chr2:99933600-99935800	Strong transcription	Osteobl	bone
50	chr2:99933600-99936000	Strong transcription	Cortex derived primary cultured neurospheres	brain

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