Variant report

Variant	rs7564587
Chromosome Location	chr2:100091313-100091314
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100080735..100084657-chr2:100090928..100093443,3	K562	blood:
2	chr2:100087595..100089096-chr2:100090818..100093356,2	K562	blood:
3	chr2:100088510..100094256-chr2:100103985..100108648,6	K562	blood:
4	chr2:100091037..100094858-chr2:100099869..100102767,4	K562	blood:

Variant related genes	Relation type
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 101 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1000409	0.83[ASN][1000 genomes]
rs1011633	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10170425	0.83[ASN][1000 genomes]
rs10172068	0.83[ASN][1000 genomes]
rs10172752	0.83[ASN][1000 genomes]
rs10186340	0.81[ASN][1000 genomes]
rs1053544	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10865031	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11884686	0.85[EUR][1000 genomes]
rs11887574	0.81[ASN][1000 genomes]
rs11892441	0.87[EUR][1000 genomes]
rs11899745	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12052986	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12465846	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13392042	0.83[ASN][1000 genomes]
rs13394688	0.81[ASN][1000 genomes]
rs13427780	0.85[ASN][1000 genomes]
rs1451246	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1584647	0.87[EUR][1000 genomes]
rs1584648	0.86[EUR][1000 genomes]
rs17022629	0.87[EUR][1000 genomes]
rs1839666	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1839667	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1901283	0.83[ASN][1000 genomes]
rs1973011	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2053917	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2122748	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2290255	0.87[EUR][1000 genomes]
rs2290261	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2309576	0.84[EUR][1000 genomes]
rs2309585	0.83[ASN][1000 genomes]
rs2309604	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2309617	0.84[EUR][1000 genomes]
rs28369943	0.83[ASN][1000 genomes]
rs28382946	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28382984	0.87[EUR][1000 genomes]
rs3087386	0.83[ASN][1000 genomes]
rs3749087	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3791212	0.84[EUR][1000 genomes]
rs3792134	0.83[ASN][1000 genomes]
rs3792137	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3792142	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3792144	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3792146	0.82[ASN][1000 genomes]
rs3792149	0.83[ASN][1000 genomes]
rs4143760	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4476396	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4851204	0.85[EUR][1000 genomes]
rs4851206	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4851208	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4851209	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs57977991	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58958283	0.87[EUR][1000 genomes]
rs59178618	0.84[EUR][1000 genomes]
rs60257640	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60335031	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61103312	0.87[EUR][1000 genomes]
rs62155809	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6542879	0.83[ASN][1000 genomes]
rs6542880	0.83[ASN][1000 genomes]
rs6542881	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542882	0.86[ASN][1000 genomes]
rs6711073	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6713608	0.83[EUR][1000 genomes]
rs6713792	0.88[ASN][1000 genomes]
rs6714244	0.88[ASN][1000 genomes]
rs6715321	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6717515	0.81[ASN][1000 genomes]
rs6720885	0.83[EUR][1000 genomes]
rs6732750	0.87[EUR][1000 genomes]
rs6737560	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6761390	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs717454	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7558062	0.85[EUR][1000 genomes]
rs7560795	0.81[ASN][1000 genomes]
rs7560996	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7563455	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7563462	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7567674	0.83[ASN][1000 genomes]
rs7572779	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7580448	0.83[ASN][1000 genomes]
rs7584127	0.87[EUR][1000 genomes]
rs7585019	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7589365	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7593274	0.87[EUR][1000 genomes]
rs7597045	0.85[EUR][1000 genomes]
rs7597141	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7598629	0.83[ASN][1000 genomes]
rs7602923	0.84[EUR][1000 genomes]
rs7606977	0.85[EUR][1000 genomes]
rs769105	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs896248	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs896249	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs959929	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	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
5	nsv874700	chr2:100062163-100099989	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv535841	chr2:100072790-100112121	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers 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	12 gene(s)	inside rSNPs	diseases
7	esv1811477	chr2:100089078-100105013	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7564587	LYG1	cis	Nerve Tibial	GTEx
rs7564587	LYG1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100055800-100092600	Weak transcription	Gastric	stomach
2	chr2:100075200-100103000	Weak transcription	Hela-S3	cervix
3	chr2:100076200-100098400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:100076200-100105000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:100076600-100094800	Weak transcription	Spleen	Spleen
6	chr2:100076600-100104200	Weak transcription	NHLF	lung
7	chr2:100078600-100092200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:100078600-100092600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr2:100078600-100096800	Weak transcription	NH-A	brain
10	chr2:100078800-100091400	Weak transcription	Adipose Nuclei	Adipose
11	chr2:100078800-100091800	Weak transcription	Fetal Kidney	kidney
12	chr2:100078800-100093200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:100078800-100101400	Weak transcription	Fetal Lung	lung
14	chr2:100078800-100103000	Weak transcription	Primary B cells from cord blood	blood
15	chr2:100078800-100105000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr2:100079000-100091400	Weak transcription	Osteobl	bone
17	chr2:100079000-100091600	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:100079200-100091600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:100079200-100092000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr2:100079200-100092600	Weak transcription	Placenta	Placenta
21	chr2:100079200-100093000	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr2:100079200-100096600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:100079200-100098400	Weak transcription	NHDF-Ad	bronchial
24	chr2:100079200-100104000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:100080400-100103200	Weak transcription	Fetal Stomach	stomach
26	chr2:100080600-100098000	Weak transcription	Dnd41	blood
27	chr2:100080800-100103200	Weak transcription	HSMM	muscle
28	chr2:100081200-100092400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr2:100085200-100091600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:100085600-100103000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr2:100086000-100102000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr2:100086200-100092600	Weak transcription	Right Atrium	heart
33	chr2:100086200-100092600	Weak transcription	Right Ventricle	heart
34	chr2:100086200-100093200	Weak transcription	Psoas Muscle	Psoas
35	chr2:100086400-100102000	Weak transcription	Thymus	Thymus
36	chr2:100087400-100091600	Enhancers	HMEC	breast
37	chr2:100087800-100091400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:100087800-100095000	Weak transcription	Primary hematopoietic stem cells	blood
39	chr2:100087800-100098400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr2:100088000-100092000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:100088000-100094800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:100088000-100104800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr2:100088200-100092000	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr2:100088200-100098200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr2:100088400-100092000	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr2:100088600-100092600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr2:100088600-100093400	Enhancers	iPS-15b Cell Line	embryonic stem cell
48	chr2:100088800-100091400	Enhancers	H1 Cell Line	embryonic stem cell
49	chr2:100088800-100091400	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr2:100088800-100091400	Enhancers	A549	lung

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