Variant report

Variant	rs3792144
Chromosome Location	chr2:100056736-100056737
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100055571..100061199-chr2:100104819..100108042,8	MCF-7	breast:
2	chr2:99950527..99953056-chr2:100056612..100059511,2	K562	blood:
3	chr2:100056180..100057892-chr2:100105208..100108122,2	K562	blood:

Variant related genes	Relation type
ENSG00000115514	Chromatin interaction
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1000409	0.88[ASN][1000 genomes]
rs1011633	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10170425	0.88[ASN][1000 genomes]
rs10172068	0.88[ASN][1000 genomes]
rs10172752	0.88[ASN][1000 genomes]
rs10173466	0.83[ASN][1000 genomes]
rs1053544	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10865031	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11884686	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11887109	0.85[ASN][1000 genomes]
rs11887574	0.80[ASN][1000 genomes]
rs11892441	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11899745	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12052986	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12464785	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12465846	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475639	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13392042	0.88[ASN][1000 genomes]
rs13394688	0.86[ASN][1000 genomes]
rs13427780	0.82[ASN][1000 genomes]
rs1451243	0.80[ASN][1000 genomes]
rs1451246	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1584647	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1584648	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17022564	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17022629	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1839666	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1839667	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1901283	0.88[ASN][1000 genomes]
rs1973011	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2053917	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2122748	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290255	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2290261	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2309576	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2309585	0.88[ASN][1000 genomes]
rs2309604	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2309617	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28369943	0.88[ASN][1000 genomes]
rs28382946	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28382984	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3087386	0.88[ASN][1000 genomes]
rs3749087	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3791212	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3792134	0.88[ASN][1000 genomes]
rs3792137	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792142	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3792146	0.87[ASN][1000 genomes]
rs3792149	0.88[ASN][1000 genomes]
rs4143760	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4476396	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851204	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4851206	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851208	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4851209	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55815229	0.81[EUR][1000 genomes]
rs57242893	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs57977991	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58086269	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58958283	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs59178618	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs59661148	0.83[AMR][1000 genomes]
rs60257640	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60335031	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61103312	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62153855	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62155809	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542879	0.88[ASN][1000 genomes]
rs6542880	0.88[ASN][1000 genomes]
rs6542881	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6542882	0.82[ASN][1000 genomes]
rs6711073	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6713608	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6713792	0.84[ASN][1000 genomes]
rs6714244	0.84[ASN][1000 genomes]
rs6715321	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717515	0.85[ASN][1000 genomes]
rs6720885	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6732750	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6737560	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6761390	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs717454	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7558062	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7560996	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7563455	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7563462	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564587	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7567674	0.88[ASN][1000 genomes]
rs7572779	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7580448	0.88[ASN][1000 genomes]
rs7584127	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7585019	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7589365	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7593274	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7597045	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7597141	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7598629	0.88[ASN][1000 genomes]
rs7602923	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7606977	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs769105	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896248	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896249	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs959929	0.88[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
rs3792144	LYG1	cis	Nerve Tibial	GTEx
rs3792144	LYG1	cis	Adipose Subcutaneous	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99999400-100056800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:100005800-100062600	Strong transcription	Dnd41	blood
3	chr2:100005800-100066000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:100006000-100081200	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr2:100021200-100077800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:100022200-100059000	Strong transcription	Liver	Liver
7	chr2:100032600-100078000	Weak transcription	Psoas Muscle	Psoas
8	chr2:100034200-100088800	Weak transcription	Small Intestine	intestine
9	chr2:100036800-100074800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr2:100038200-100063200	Weak transcription	Fetal Intestine Small	intestine
11	chr2:100038200-100073800	Weak transcription	Esophagus	oesophagus
12	chr2:100041400-100077800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr2:100041600-100083400	Weak transcription	Brain Substantia Nigra	brain
14	chr2:100042800-100065000	Weak transcription	Lung	lung
15	chr2:100045000-100064200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr2:100045400-100068200	Weak transcription	Ovary	ovary
17	chr2:100047800-100063200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:100048200-100090600	Weak transcription	Stomach Mucosa	stomach
19	chr2:100048400-100067800	Weak transcription	Fetal Heart	heart
20	chr2:100048600-100064000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:100048600-100068200	Weak transcription	Spleen	Spleen
22	chr2:100048800-100070400	Weak transcription	Fetal Brain Female	brain
23	chr2:100050000-100065000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:100051800-100064600	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr2:100052600-100059200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:100052800-100057800	Strong transcription	Adipose Nuclei	Adipose
27	chr2:100052800-100059000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr2:100052800-100059000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr2:100052800-100059200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr2:100053000-100058400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:100053000-100059600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:100053200-100059000	Strong transcription	Fetal Intestine Large	intestine
33	chr2:100053400-100058200	Strong transcription	Primary B cells from cord blood	blood
34	chr2:100053400-100059800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr2:100053600-100059200	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:100053600-100059400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr2:100053600-100059600	Strong transcription	HepG2	liver
38	chr2:100053800-100059200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:100053800-100059200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr2:100053800-100075800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:100054400-100058400	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:100054400-100059000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr2:100054400-100059600	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr2:100054600-100056800	Strong transcription	NHDF-Ad	bronchial
45	chr2:100054600-100057400	Strong transcription	Hela-S3	cervix
46	chr2:100054600-100057800	Strong transcription	HUVEC	blood vessel
47	chr2:100054600-100059000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr2:100054600-100059000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:100054600-100059200	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr2:100054600-100059200	Strong transcription	HSMM	muscle

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