Variant report

Variant	rs72815074
Chromosome Location	chr2:99989348-99989349
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99977104..99978712-chr2:99988658..99990955,2	MCF-7	breast:

Extended variants
information (count: 104 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:99)

rs_ID	r²[population]
rs10173883	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10175852	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10176205	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179343	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179435	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10179697	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180138	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10180688	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10182492	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs10186223	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191001	0.88[ASN][1000 genomes]
rs10207435	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210257	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10210346	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10496337	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123776	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123778	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123783	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12162367	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12617324	0.92[EUR][1000 genomes]
rs12623835	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12989521	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12991982	0.83[AMR][1000 genomes]
rs12992356	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13001438	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13017843	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13028722	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032885	0.82[EUR][1000 genomes]
rs13384665	0.94[ASN][1000 genomes]
rs13394927	0.84[EUR][1000 genomes]
rs13401163	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13402784	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs13405400	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13409359	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13415713	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13416265	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13419448	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420087	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420293	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs13426758	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13427424	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429185	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13429806	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13430662	0.81[ASN][1000 genomes]
rs13430962	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13432046	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17022653	0.84[EUR][1000 genomes]
rs17022663	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1882598	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1922625	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1922626	0.85[EUR][1000 genomes]
rs1922627	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1948101	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2309577	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309615	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2309616	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28369949	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382945	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382947	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28382955	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs28745279	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3087399	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792151	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3828162	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4522654	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4850902	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851197	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851199	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851201	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851202	0.83[EUR][1000 genomes]
rs6542877	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6706425	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712137	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721031	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6726711	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744199	0.85[EUR][1000 genomes]
rs6745645	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6749029	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72815086	0.81[EUR][1000 genomes]
rs7567230	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7567462	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7569805	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579143	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579171	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7581337	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582085	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582133	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584022	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7584705	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7585532	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7599384	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7599843	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7603388	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7606279	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9308819	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9308821	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308822	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9308823	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973846	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[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	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
4	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
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs72815074	LYG1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99956200-100004800	Weak transcription	Fetal Heart	heart
2	chr2:99957600-99989400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:99975400-100006400	Weak transcription	Stomach Mucosa	stomach
4	chr2:99976000-99989600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
5	chr2:99976200-100003800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr2:99976200-100004400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr2:99976400-100003200	Strong transcription	Monocytes-CD14+_RO01746	blood
8	chr2:99976600-100002400	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr2:99976600-100004800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr2:99976800-99989600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:99977000-99991000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr2:99977000-99996800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:99977000-100001000	Strong transcription	Primary B cells from cord blood	blood
14	chr2:99977000-100001400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:99977000-100003200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:99977000-100003200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr2:99977000-100003600	Strong transcription	Primary T helper cells PMA-I stimulated	--
18	chr2:99977000-100003800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:99977000-100003800	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:99977200-99989600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:99977200-99991000	Strong transcription	Dnd41	blood
22	chr2:99977200-99996200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr2:99977600-99997000	Strong transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:99977600-100002200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:99977600-100003600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr2:99977800-99989800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr2:99977800-99989800	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr2:99977800-99989800	Strong transcription	Fetal Intestine Large	intestine
29	chr2:99977800-99996800	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr2:99978200-99990600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr2:99978200-99997200	Strong transcription	Placenta	Placenta
32	chr2:99978200-100011800	Weak transcription	Esophagus	oesophagus
33	chr2:99978400-99989600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:99978400-99989600	Weak transcription	Spleen	Spleen
35	chr2:99978600-99995600	Weak transcription	Small Intestine	intestine
36	chr2:99979200-99990600	Strong transcription	Left Ventricle	heart
37	chr2:99979400-99990600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr2:99979400-99991000	Strong transcription	Primary T cells from cord blood	blood
39	chr2:99979400-99999800	Strong transcription	Osteobl	bone
40	chr2:99979400-100001600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr2:99979400-100003600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr2:99979400-100004200	Strong transcription	Fetal Thymus	thymus
43	chr2:99979600-99989800	Strong transcription	HMEC	breast
44	chr2:99979600-99990000	Strong transcription	HUVEC	blood vessel
45	chr2:99979600-99990200	Strong transcription	NH-A	brain
46	chr2:99979600-99990600	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr2:99979600-99992200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
48	chr2:99979600-99997200	Strong transcription	Adipose Nuclei	Adipose
49	chr2:99979600-100002800	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:99979600-100003200	Strong transcription	Rectal Mucosa Donor 29	rectum

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