Variant report

Variant	rs61103312
Chromosome Location	chr2:100005612-100005613
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs1011633	0.89[EUR][1000 genomes]
rs10187843	0.84[ASN][1000 genomes]
rs1053544	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10865031	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11123786	0.82[ASN][1000 genomes]
rs11679115	0.80[ASN][1000 genomes]
rs11683651	0.80[ASN][1000 genomes]
rs11884686	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11892441	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11899745	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11902994	0.80[ASN][1000 genomes]
rs12052986	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12464535	0.80[ASN][1000 genomes]
rs12464785	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12465846	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12475639	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12623540	0.80[ASN][1000 genomes]
rs13018274	0.83[ASN][1000 genomes]
rs13389623	0.82[ASN][1000 genomes]
rs1376443	0.80[ASN][1000 genomes]
rs1451246	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1584647	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1584648	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17022564	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17022629	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1807985	0.82[ASN][1000 genomes]
rs1839666	0.87[EUR][1000 genomes]
rs1839667	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1973011	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2053917	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2122748	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2242037	0.82[ASN][1000 genomes]
rs2290255	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290256	0.83[ASN][1000 genomes]
rs2290261	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305354	0.82[ASN][1000 genomes]
rs2309576	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2309604	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2309617	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28382946	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28382984	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3749087	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3791212	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3792137	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3792142	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3792144	0.85[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	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4535093	0.82[ASN][1000 genomes]
rs4850903	0.80[ASN][1000 genomes]
rs4851204	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4851205	0.82[ASN][1000 genomes]
rs4851206	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4851208	0.85[EUR][1000 genomes]
rs55815229	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57242893	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57977991	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58086269	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58958283	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59178618	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59661148	0.98[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60257640	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62153855	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62155809	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6542881	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6711073	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6713608	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6715321	0.85[EUR][1000 genomes]
rs6720885	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6732750	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6737560	0.87[EUR][1000 genomes]
rs6761390	0.85[EUR][1000 genomes]
rs717454	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7558062	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7558074	0.80[ASN][1000 genomes]
rs7560996	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7561079	0.86[ASN][1000 genomes]
rs7563455	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7563462	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7564587	0.87[EUR][1000 genomes]
rs7572779	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7574135	0.84[ASN][1000 genomes]
rs7579403	0.82[ASN][1000 genomes]
rs7584127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585019	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7585721	0.80[ASN][1000 genomes]
rs7586892	0.86[ASN][1000 genomes]
rs7587419	0.86[ASN][1000 genomes]
rs7589365	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7591212	0.80[ASN][1000 genomes]
rs7593274	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7597045	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7597141	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7601470	0.80[ASN][1000 genomes]
rs7601730	0.82[ASN][1000 genomes]
rs7602923	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7606977	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs769105	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs896248	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs896249	0.80[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
rs61103312	LYG1	cis	Skin Sun Exposed Lower leg	GTEx
rs61103312	LYG1	cis	Adipose Subcutaneous	GTEx
rs61103312	LYG1	cis	Nerve Tibial	GTEx
rs61103312	REV1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99975400-100006400	Weak transcription	Stomach Mucosa	stomach
2	chr2:99978200-100011800	Weak transcription	Esophagus	oesophagus
3	chr2:99979600-100009600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:99983200-100013600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:99985600-100006800	Weak transcription	Colonic Mucosa	Colon
6	chr2:99990000-100006600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:99990000-100012200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:99990200-100010800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:99990600-100006600	Weak transcription	Pancreas	Pancrea
10	chr2:99990600-100010800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:99990600-100010800	Weak transcription	Spleen	Spleen
12	chr2:99990800-100007000	Weak transcription	Gastric	stomach
13	chr2:99993200-100006600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr2:99994200-100010000	Weak transcription	Brain Substantia Nigra	brain
15	chr2:99994200-100010800	Weak transcription	Fetal Brain Male	brain
16	chr2:99994200-100011400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr2:99996600-100009400	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr2:99996800-100010000	Weak transcription	Small Intestine	intestine
19	chr2:99997200-100009000	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr2:99997200-100011000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:99998800-100007000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr2:99999000-100006600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr2:99999200-100008800	Strong transcription	HepG2	liver
24	chr2:99999400-100056800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr2:99999600-100006600	Weak transcription	HMEC	breast
26	chr2:100000000-100006000	Weak transcription	HUVEC	blood vessel
27	chr2:100000000-100014800	Weak transcription	Psoas Muscle	Psoas
28	chr2:100000200-100006200	Weak transcription	Hela-S3	cervix
29	chr2:100000200-100006600	Weak transcription	NHEK	skin
30	chr2:100000200-100007000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr2:100000400-100006600	Weak transcription	Brain Anterior Caudate	brain
32	chr2:100000400-100006800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr2:100000400-100007000	Weak transcription	Brain Cingulate Gyrus	brain
34	chr2:100000400-100009400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:100001000-100007000	Weak transcription	Fetal Kidney	kidney
36	chr2:100001000-100022000	Weak transcription	Pancreatic Islets	Pancreatic Islet
37	chr2:100001200-100006400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr2:100001200-100006600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr2:100001200-100006600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr2:100001200-100007000	Weak transcription	Brain Germinal Matrix	brain
41	chr2:100001200-100007000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:100001200-100007000	Weak transcription	Colon Smooth Muscle	Colon
43	chr2:100001400-100006000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr2:100001400-100006000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr2:100001400-100006000	Weak transcription	GM12878-XiMat	blood
46	chr2:100001400-100006400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:100001400-100006400	Weak transcription	Fetal Brain Female	brain
48	chr2:100001400-100006600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr2:100001400-100006600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:100001400-100006600	Weak transcription	K562	blood

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