Variant report

Variant	rs6744199
Chromosome Location	chr2:99893775-99893776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10173883	0.81[EUR][1000 genomes]
rs10175852	0.82[EUR][1000 genomes]
rs10176205	0.81[EUR][1000 genomes]
rs10179435	0.83[EUR][1000 genomes]
rs10179697	0.81[EUR][1000 genomes]
rs10180138	0.83[EUR][1000 genomes]
rs10180688	0.85[EUR][1000 genomes]
rs10186223	0.83[EUR][1000 genomes]
rs10207435	0.83[EUR][1000 genomes]
rs10210257	0.83[EUR][1000 genomes]
rs10210346	0.83[EUR][1000 genomes]
rs10496337	0.83[EUR][1000 genomes]
rs11123769	0.81[EUR][1000 genomes]
rs11123776	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11123778	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11123783	0.87[EUR][1000 genomes]
rs12162367	0.87[EUR][1000 genomes]
rs12617324	0.89[EUR][1000 genomes]
rs12623835	0.87[EUR][1000 genomes]
rs12992356	0.88[EUR][1000 genomes]
rs12993310	0.84[EUR][1000 genomes]
rs13001438	0.87[EUR][1000 genomes]
rs13017843	0.86[EUR][1000 genomes]
rs13028722	0.87[EUR][1000 genomes]
rs13032885	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13401163	0.85[EUR][1000 genomes]
rs13405400	0.81[EUR][1000 genomes]
rs13409359	0.83[EUR][1000 genomes]
rs13415713	0.81[EUR][1000 genomes]
rs13416265	0.82[EUR][1000 genomes]
rs13419448	0.83[EUR][1000 genomes]
rs13420087	0.81[EUR][1000 genomes]
rs13426758	0.85[EUR][1000 genomes]
rs13427424	0.82[EUR][1000 genomes]
rs13429185	0.85[EUR][1000 genomes]
rs13429806	0.83[EUR][1000 genomes]
rs13430962	0.81[EUR][1000 genomes]
rs13432046	0.83[EUR][1000 genomes]
rs1487271	0.84[EUR][1000 genomes]
rs1565054	0.86[EUR][1000 genomes]
rs1843807	0.84[EUR][1000 genomes]
rs1882598	0.87[EUR][1000 genomes]
rs1922625	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1922627	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1948101	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2309577	0.87[EUR][1000 genomes]
rs2309615	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2309616	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28369949	0.82[EUR][1000 genomes]
rs28382945	0.85[EUR][1000 genomes]
rs28382947	0.85[EUR][1000 genomes]
rs28745279	0.85[EUR][1000 genomes]
rs3087399	0.83[EUR][1000 genomes]
rs3828162	0.87[EUR][1000 genomes]
rs4522654	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4850902	0.87[EUR][1000 genomes]
rs4851191	0.84[EUR][1000 genomes]
rs4851194	0.84[EUR][1000 genomes]
rs4851197	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4851199	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4851201	0.88[EUR][1000 genomes]
rs6542876	0.80[EUR][1000 genomes]
rs6542877	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6706425	0.87[EUR][1000 genomes]
rs6712137	0.87[EUR][1000 genomes]
rs6721031	0.87[EUR][1000 genomes]
rs6726711	0.87[EUR][1000 genomes]
rs6745645	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6749029	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72815074	0.85[EUR][1000 genomes]
rs7567230	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7567462	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7569805	0.88[EUR][1000 genomes]
rs7579143	0.87[EUR][1000 genomes]
rs7579171	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7579999	0.86[EUR][1000 genomes]
rs7581337	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7582085	0.83[EUR][1000 genomes]
rs7582133	0.83[EUR][1000 genomes]
rs7584022	0.90[EUR][1000 genomes]
rs7584705	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7599384	0.87[EUR][1000 genomes]
rs7599843	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7602401	0.84[EUR][1000 genomes]
rs7603388	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7606279	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9308819	0.85[EUR][1000 genomes]
rs9308821	0.83[EUR][1000 genomes]
rs9308822	0.81[EUR][1000 genomes]
rs9308823	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 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	nsv515702	chr2:99827733-99922967	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	nsv458685	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv582519	chr2:99827733-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	nsv874698	chr2:99827733-99924918	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
6	nsv1001784	chr2:99838079-99910328	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv535840	chr2:99838079-99910328	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
8	nsv458696	chr2:99838203-99922967	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	nsv582520	chr2:99838203-99922967	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv997436	chr2:99840131-99916886	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv1009872	chr2:99840131-99924543	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
12	nsv1001194	chr2:99840131-99928323	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
13	esv2762746	chr2:99840143-99916898	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
14	nsv1005118	chr2:99841951-99924543	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
15	nsv1001736	chr2:99846306-99916886	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
16	nsv1009459	chr2:99846306-99918895	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
17	nsv1002169	chr2:99846306-99924543	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
18	esv2751904	chr2:99847882-99913998	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
19	nsv1001235	chr2:99847890-99913998	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
20	nsv582521	chr2:99847890-99922967	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
21	nsv1007566	chr2:99847890-99924543	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
22	nsv999059	chr2:99847890-99926934	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
23	nsv1007249	chr2:99855978-99916886	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
24	nsv1004291	chr2:99855978-99919999	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
25	nsv1010419	chr2:99857259-99897312	Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
26	nsv1003262	chr2:99858556-99924543	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6744199	LYG1	cis	Whole Blood	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99860400-99899800	Weak transcription	Psoas Muscle	Psoas
2	chr2:99861200-99900800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:99861800-99899400	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:99873800-99900600	Weak transcription	Ovary	ovary
5	chr2:99879000-99933600	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:99880400-99900000	Weak transcription	Stomach Smooth Muscle	stomach
7	chr2:99880400-99907400	Weak transcription	Right Ventricle	heart
8	chr2:99888200-99895600	Weak transcription	Fetal Brain Female	brain
9	chr2:99889000-99906000	Weak transcription	Aorta	Aorta
10	chr2:99890800-99895000	Weak transcription	HSMMtube	muscle
11	chr2:99892400-99900000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr2:99892400-99900600	Weak transcription	Brain Hippocampus Middle	brain
13	chr2:99892400-99918600	Weak transcription	Brain Anterior Caudate	brain
14	chr2:99892400-99935000	Weak transcription	Brain Angular Gyrus	brain
15	chr2:99892600-99896600	Weak transcription	Fetal Muscle Leg	muscle
16	chr2:99892600-99900000	Weak transcription	Brain Germinal Matrix	brain
17	chr2:99892800-99895400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr2:99892800-99896200	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:99892800-99900800	Weak transcription	Brain Inferior Temporal Lobe	brain

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