Variant report

Variant	rs62155769
Chromosome Location	chr2:99978950-99978951
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99952304..99954680-chr2:99976875..99979040,2	K562	blood:
2	chr2:99971535..99975778-chr2:99978394..99981073,4	K562	blood:
3	chr2:99971535..99975686-chr2:99976476..99979996,5	K562	blood:
4	chr2:99977638..99980361-chr2:99981242..99982894,2	K562	blood:
5	chr2:99952346..99954433-chr2:99975150..99979293,3	K562	blood:

Variant related genes	Relation type
ENSG00000115514	Chromatin interaction
ENSG00000158417	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10496336	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11885942	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11893359	0.86[EUR][1000 genomes]
rs11896520	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12474305	0.81[AMR][1000 genomes]
rs2141907	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2305352	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2309618	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28369945	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28382977	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3087403	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3792143	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3792150	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4851203	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61436115	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62153852	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62155807	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6714650	0.85[AMR][1000 genomes]
rs6748200	0.82[AMR][1000 genomes]
rs737094	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	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	nsv524466	chr2:99952086-100031551	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62155769	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	chr2:99955000-99979200	Weak transcription	Fetal Stomach	stomach
2	chr2:99955000-99979800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr2:99955200-99979600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr2:99955200-99982600	Weak transcription	Fetal Brain Male	brain
5	chr2:99955400-99979600	Weak transcription	Primary hematopoietic stem cells	blood
6	chr2:99955400-99979600	Weak transcription	NH-A	brain
7	chr2:99956200-100004800	Weak transcription	Fetal Heart	heart
8	chr2:99956400-99979600	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr2:99956400-99979600	Weak transcription	HUVEC	blood vessel
10	chr2:99957600-99989400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:99958200-99979600	Weak transcription	A549	lung
12	chr2:99959800-99980000	Weak transcription	Lung	lung
13	chr2:99961200-99979400	Weak transcription	Ovary	ovary
14	chr2:99962400-99979800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:99962400-99979800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr2:99965600-99979800	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:99969400-99981600	Weak transcription	Fetal Brain Female	brain
18	chr2:99970800-99979200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr2:99970800-99979600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr2:99970800-99979600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr2:99970800-99979800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:99970800-99979800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr2:99971000-99979600	Weak transcription	HMEC	breast
24	chr2:99973200-99979800	Weak transcription	Aorta	Aorta
25	chr2:99973400-99979600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr2:99973400-99979600	Weak transcription	Brain Hippocampus Middle	brain
27	chr2:99973400-99979800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr2:99973400-99982600	Weak transcription	Psoas Muscle	Psoas
29	chr2:99973800-99979800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:99973800-99982200	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr2:99974200-99979400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr2:99974200-99979800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr2:99974400-99979800	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:99974400-99979800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr2:99974400-99979800	Weak transcription	HSMMtube	muscle
36	chr2:99974400-99981600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr2:99974800-99984000	Weak transcription	Pancreas	Pancrea
38	chr2:99975000-99979800	Weak transcription	Gastric	stomach
39	chr2:99975000-99981800	Weak transcription	Thymus	Thymus
40	chr2:99975200-99980800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr2:99975200-99980800	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr2:99975400-99979800	Weak transcription	Fetal Lung	lung
43	chr2:99975400-99979800	Weak transcription	NHLF	lung
44	chr2:99975400-100006400	Weak transcription	Stomach Mucosa	stomach
45	chr2:99975800-99979800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr2:99976000-99989600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr2:99976200-100003800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr2:99976200-100004400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr2:99976400-99979600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr2:99976400-99979600	Weak transcription	Fetal Muscle Leg	muscle

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