Variant report

Variant	rs58958283
Chromosome Location	chr2:100009924-100009925
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HNF4A	chr2:100009853-100010174	HepG2	liver:	n/a	chr2:100010029-100010042 chr2:100010030-100010042 chr2:100010030-100010042 chr2:100010028-100010043 chr2:100010028-100010043 chr2:100010028-100010043 chr2:100010030-100010042 chr2:100010028-100010043 chr2:100010028-100010043 chr2:100010029-100010037
2	MAX	chr2:100009806-100010390	HepG2	liver:	n/a	n/a
3	CEBPB	chr2:100009896-100010175	HepG2	liver:	n/a	n/a
4	POLR2A	chr2:100009821-100010005	Hela-S3	cervix:	n/a	n/a
5	HNF4A	chr2:100009861-100010233	HepG2	liver:	n/a	chr2:100010029-100010042 chr2:100010030-100010042 chr2:100010030-100010042 chr2:100010028-100010043 chr2:100010028-100010043 chr2:100010028-100010043 chr2:100010030-100010042 chr2:100010028-100010043 chr2:100010028-100010043 chr2:100010029-100010037
6	MXI1	chr2:100009908-100010314	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100007416..100010173-chr2:100015934..100018693,2	MCF-7	breast:
2	chr2:100008715..100012637-chr2:100019428..100022260,4	K562	blood:

Variant related genes	Relation type
EIF5B	TF binding region
ENSG00000273306	Chromatin interaction
ENSG00000135945	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs1011633	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10187843	0.84[ASN][1000 genomes]
rs1053544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10865031	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11123786	0.82[ASN][1000 genomes]
rs11884686	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11892441	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11899745	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12052986	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12464785	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12465846	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12475639	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13389623	0.83[ASN][1000 genomes]
rs1451246	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1584647	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1584648	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17022564	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17022629	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1839666	0.87[EUR][1000 genomes]
rs1839667	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1973011	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2053917	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2122748	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2242037	0.82[ASN][1000 genomes]
rs2290255	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2290256	0.80[ASN][1000 genomes]
rs2290261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305354	0.82[ASN][1000 genomes]
rs2309576	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2309604	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2309617	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28382946	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28382984	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3749087	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791212	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3792137	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3792142	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3792144	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3792152	0.80[ASN][1000 genomes]
rs3828316	0.82[ASN][1000 genomes]
rs4143760	0.87[EUR][1000 genomes]
rs4476396	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4535093	0.82[ASN][1000 genomes]
rs4851204	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4851205	0.82[ASN][1000 genomes]
rs4851206	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851208	0.85[EUR][1000 genomes]
rs55815229	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57242893	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57977991	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58086269	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59178618	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59661148	0.97[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs60257640	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60335031	0.80[AMR][1000 genomes]
rs61103312	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62153855	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62155809	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6542881	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6711073	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6713608	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6715321	0.85[EUR][1000 genomes]
rs6720885	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6732750	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6737560	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6761390	0.85[EUR][1000 genomes]
rs717454	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7558062	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7560996	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7561079	0.83[ASN][1000 genomes]
rs7563455	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7563462	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7564587	0.87[EUR][1000 genomes]
rs7572779	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7574135	0.84[ASN][1000 genomes]
rs7579403	0.82[ASN][1000 genomes]
rs7584127	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7585019	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7586892	0.83[ASN][1000 genomes]
rs7587419	0.83[ASN][1000 genomes]
rs7589365	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7593274	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7597045	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7597141	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7601730	0.82[ASN][1000 genomes]
rs7602923	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7606977	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs769105	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs896248	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs896249	0.81[AMR][1000 genomes];0.87[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
rs58958283	REV1	Cis_1M	lymphoblastoid	RTeQTL
rs58958283	LYG1	cis	Adipose Subcutaneous	GTEx
rs58958283	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs58958283	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	chr2:99978200-100011800	Weak transcription	Esophagus	oesophagus
2	chr2:99983200-100013600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:99990000-100012200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:99990200-100010800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:99990600-100010800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:99990600-100010800	Weak transcription	Spleen	Spleen
7	chr2:99994200-100010000	Weak transcription	Brain Substantia Nigra	brain
8	chr2:99994200-100010800	Weak transcription	Fetal Brain Male	brain
9	chr2:99994200-100011400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:99996800-100010000	Weak transcription	Small Intestine	intestine
11	chr2:99997200-100011000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
12	chr2:99999400-100056800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr2:100000000-100014800	Weak transcription	Psoas Muscle	Psoas
14	chr2:100001000-100022000	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr2:100001400-100010000	Weak transcription	Brain Angular Gyrus	brain
16	chr2:100001400-100010600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr2:100003600-100010800	Weak transcription	Lung	lung
18	chr2:100003600-100011400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:100004800-100023000	Strong transcription	Primary B cells from cord blood	blood
20	chr2:100004800-100044800	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr2:100005200-100049800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr2:100005400-100020000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr2:100005600-100045400	Strong transcription	Primary T cells from cord blood	blood
24	chr2:100005800-100016600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr2:100005800-100019600	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr2:100005800-100019600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
27	chr2:100005800-100045200	Strong transcription	Primary T cells fromperipheralblood	blood
28	chr2:100005800-100062600	Strong transcription	Dnd41	blood
29	chr2:100005800-100066000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr2:100006000-100012200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:100006000-100019000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:100006000-100019200	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr2:100006000-100019200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr2:100006000-100019600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr2:100006000-100023400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr2:100006000-100026200	Strong transcription	HUVEC	blood vessel
37	chr2:100006000-100034200	Strong transcription	GM12878-XiMat	blood
38	chr2:100006000-100046400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:100006000-100049600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:100006000-100050800	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr2:100006000-100051000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr2:100006000-100081200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr2:100006200-100017800	Strong transcription	Hela-S3	cervix
44	chr2:100006200-100019000	Strong transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:100006200-100019800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:100006200-100023600	Strong transcription	Fetal Thymus	thymus
47	chr2:100006200-100028600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:100006200-100046400	Strong transcription	Primary B cells from peripheral blood	blood
49	chr2:100006200-100051400	Strong transcription	Primary T helper cells fromperipheralblood	blood
50	chr2:100006400-100016400	Strong transcription	A549	lung

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