Variant report

Variant	rs7589365
Chromosome Location	chr2:99990324-99990325
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99984624..99988612-chr2:99989549..99993377,4	MCF-7	breast:
2	chr2:99990124..99992990-chr2:99997143..100000018,2	MCF-7	breast:
3	chr2:99977104..99978712-chr2:99988658..99990955,2	MCF-7	breast:

Extended variants
information (count: 103 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs1011633	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10187843	0.81[ASN][1000 genomes]
rs1053544	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10865031	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11679115	0.89[ASN][1000 genomes]
rs11683651	0.89[ASN][1000 genomes]
rs11884686	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11892441	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11899745	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11902994	0.89[ASN][1000 genomes]
rs12052986	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12464535	0.89[ASN][1000 genomes]
rs12464785	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12465846	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12475639	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12623540	0.89[ASN][1000 genomes]
rs13018274	0.85[ASN][1000 genomes]
rs1376443	0.89[ASN][1000 genomes]
rs1451246	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1584647	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1584648	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17022564	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17022629	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1807985	0.85[ASN][1000 genomes]
rs1839666	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1839667	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1973011	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2053917	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2122748	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2290255	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290256	0.86[ASN][1000 genomes]
rs2290261	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2309576	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2309604	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2309617	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28382946	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28382984	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3749087	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3791212	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3792137	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3792142	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3792144	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3811555	0.81[ASN][1000 genomes]
rs4143760	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4476396	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4850903	0.89[ASN][1000 genomes]
rs4851204	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851206	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4851208	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4851209	0.83[EUR][1000 genomes]
rs55815229	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57242893	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57977991	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58086269	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58958283	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59178618	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59661148	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs60257640	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60335031	0.87[AMR][1000 genomes]
rs61103312	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62153855	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62155809	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6542881	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6708861	0.81[ASN][1000 genomes]
rs6711073	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6713608	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6715321	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6720885	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6732750	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6734290	0.80[ASN][1000 genomes]
rs6737560	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6761390	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs717454	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7558062	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7558074	0.89[ASN][1000 genomes]
rs7560996	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7561079	0.83[ASN][1000 genomes]
rs7563455	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7563462	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7564587	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7571202	0.80[ASN][1000 genomes]
rs7572779	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7574135	0.81[ASN][1000 genomes]
rs7584127	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7585019	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7585721	0.89[ASN][1000 genomes]
rs7586892	0.83[ASN][1000 genomes]
rs7587419	0.83[ASN][1000 genomes]
rs7591212	0.89[ASN][1000 genomes]
rs7593274	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7597045	0.98[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7597141	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7601470	0.89[ASN][1000 genomes]
rs7602923	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7606977	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs769105	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs896248	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs896249	0.88[AMR][1000 genomes];0.91[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7589365	LYG1	cis	Nerve Tibial	GTEx
rs7589365	LYG1	cis	Adipose Subcutaneous	GTEx
rs7589365	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs7589365	REV1	Cis_1M	lymphoblastoid	RTeQTL

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	chr2:99975400-100006400	Weak transcription	Stomach Mucosa	stomach
3	chr2:99976200-100003800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:99976200-100004400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:99976400-100003200	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr2:99976600-100002400	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr2:99976600-100004800	Strong transcription	Primary B cells from peripheral blood	blood
8	chr2:99977000-99991000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:99977000-99996800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr2:99977000-100001000	Strong transcription	Primary B cells from cord blood	blood
11	chr2:99977000-100001400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:99977000-100003200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:99977000-100003200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr2:99977000-100003600	Strong transcription	Primary T helper cells PMA-I stimulated	--
15	chr2:99977000-100003800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr2:99977000-100003800	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr2:99977200-99991000	Strong transcription	Dnd41	blood
18	chr2:99977200-99996200	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr2:99977600-99997000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:99977600-100002200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr2:99977600-100003600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr2:99977800-99996800	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr2:99978200-99990600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr2:99978200-99997200	Strong transcription	Placenta	Placenta
25	chr2:99978200-100011800	Weak transcription	Esophagus	oesophagus
26	chr2:99978600-99995600	Weak transcription	Small Intestine	intestine
27	chr2:99979200-99990600	Strong transcription	Left Ventricle	heart
28	chr2:99979400-99990600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr2:99979400-99991000	Strong transcription	Primary T cells from cord blood	blood
30	chr2:99979400-99999800	Strong transcription	Osteobl	bone
31	chr2:99979400-100001600	Strong transcription	Duodenum Mucosa	Duodenum
32	chr2:99979400-100003600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
33	chr2:99979400-100004200	Strong transcription	Fetal Thymus	thymus
34	chr2:99979600-99990600	Strong transcription	H1 Cell Line	embryonic stem cell
35	chr2:99979600-99992200	Strong transcription	Primary T killer memory cells from peripheral blood	blood
36	chr2:99979600-99997200	Strong transcription	Adipose Nuclei	Adipose
37	chr2:99979600-100002800	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:99979600-100003200	Strong transcription	Rectal Mucosa Donor 29	rectum
39	chr2:99979600-100009600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr2:99979800-99996400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr2:99979800-100002200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr2:99979800-100002800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr2:99980000-99990400	Weak transcription	Gastric	stomach
44	chr2:99980600-99994400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr2:99982800-99993800	Weak transcription	Right Ventricle	heart
46	chr2:99982800-100000400	Strong transcription	HSMM	muscle
47	chr2:99983000-99993800	Strong transcription	GM12878-XiMat	blood
48	chr2:99983200-99991800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:99983200-100013600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
50	chr2:99983400-99991800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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