Variant report

Variant	rs2122748
Chromosome Location	chr2:100065369-100065370
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:100065120..100066698-chr2:100069712..100072523,2	MCF-7	breast:
2	chr2:100065327..100067396-chr2:100072129..100074926,2	K562	blood:
3	chr2:100061358..100063213-chr2:100063988..100066181,2	MCF-7	breast:
4	chr2:100064922..100067755-chr2:100103657..100105818,3	MCF-7	breast:

Extended variants
information (count: 109 )
Associated
traits (count: 2 )

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

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

Variant overlapped rSNPs/rCNVs (count:6 , 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	esv1792220	chr2:100063440-100077327	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2122748	LYG1	cis	Adipose Subcutaneous	GTEx
rs2122748	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	chr2:100005800-100066000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:100006000-100081200	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr2:100021200-100077800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:100032600-100078000	Weak transcription	Psoas Muscle	Psoas
5	chr2:100034200-100088800	Weak transcription	Small Intestine	intestine
6	chr2:100036800-100074800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr2:100038200-100073800	Weak transcription	Esophagus	oesophagus
8	chr2:100041400-100077800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:100041600-100083400	Weak transcription	Brain Substantia Nigra	brain
10	chr2:100045400-100068200	Weak transcription	Ovary	ovary
11	chr2:100048200-100090600	Weak transcription	Stomach Mucosa	stomach
12	chr2:100048400-100067800	Weak transcription	Fetal Heart	heart
13	chr2:100048600-100068200	Weak transcription	Spleen	Spleen
14	chr2:100048800-100070400	Weak transcription	Fetal Brain Female	brain
15	chr2:100053800-100075800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr2:100055400-100083200	Weak transcription	Right Ventricle	heart
17	chr2:100055600-100065400	Weak transcription	Brain Germinal Matrix	brain
18	chr2:100055600-100068600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr2:100055600-100071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr2:100055600-100078200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:100055600-100079800	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr2:100055800-100067800	Weak transcription	Fetal Lung	lung
23	chr2:100055800-100072200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr2:100055800-100072800	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr2:100055800-100076200	Weak transcription	Aorta	Aorta
26	chr2:100055800-100076400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:100055800-100089000	Weak transcription	Pancreas	Pancrea
28	chr2:100055800-100092600	Weak transcription	Gastric	stomach
29	chr2:100056600-100091000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr2:100057000-100071600	Weak transcription	H1 Cell Line	embryonic stem cell
31	chr2:100057200-100073000	Weak transcription	NHLF	lung
32	chr2:100057200-100076000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:100057400-100066800	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:100057400-100068200	Weak transcription	Hela-S3	cervix
35	chr2:100057400-100071600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr2:100057400-100077800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr2:100057400-100078000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr2:100058200-100077800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr2:100059000-100068600	Weak transcription	Brain Anterior Caudate	brain
40	chr2:100059200-100067600	Weak transcription	HSMM	muscle
41	chr2:100059200-100067800	Weak transcription	Primary hematopoietic stem cells	blood
42	chr2:100059600-100071400	Weak transcription	K562	blood
43	chr2:100060400-100079200	Strong transcription	Primary monocytes fromperipheralblood	blood
44	chr2:100060600-100065800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:100061800-100065600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:100061800-100079200	Strong transcription	Primary T cells fromperipheralblood	blood
47	chr2:100061800-100079400	Strong transcription	Liver	Liver
48	chr2:100062000-100067000	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr2:100062200-100066400	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr2:100062200-100070600	Strong transcription	Primary T cells from cord blood	blood

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