Variant report

Variant	rs1992167
Chromosome Location	chr2:20127354-20127355
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MATN3-2	chr2:20127098-20127753	NONHSAT069414

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1056233	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1115275	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11680554	0.82[EUR][1000 genomes]
rs11683973	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11688098	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11688680	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11693384	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11694821	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12988913	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12990087	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12996974	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13001254	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13005512	0.82[EUR][1000 genomes]
rs13006748	0.93[ASN][1000 genomes]
rs13011870	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13035048	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1370585	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16987220	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16987257	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17695872	0.80[EUR][1000 genomes]
rs1921731	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2028208	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34400777	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34425205	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34459327	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35307726	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35425971	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35973216	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4294960	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66496755	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6706311	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720011	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67653248	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67724270	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs721932	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs721933	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73214266	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs957614	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[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	nsv873712	chr2:19955245-20131079	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv873713	chr2:19955245-20144372	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
3	nsv873715	chr2:20059323-20144372	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases
4	nsv521619	chr2:20098208-20150817	Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv527453	chr2:20109061-20160209	ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20102600-20127600	Weak transcription	Fetal Muscle Leg	muscle
2	chr2:20102600-20127800	Weak transcription	Aorta	Aorta
3	chr2:20102600-20128000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:20102800-20127600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr2:20102800-20127600	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:20102800-20128800	Weak transcription	Liver	Liver
7	chr2:20102800-20128800	Weak transcription	Brain Germinal Matrix	brain
8	chr2:20102800-20129000	Weak transcription	Brain Anterior Caudate	brain
9	chr2:20102800-20173200	Weak transcription	Fetal Brain Male	brain
10	chr2:20103000-20127400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:20105000-20127400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:20105400-20129000	Weak transcription	Primary T cells from cord blood	blood
13	chr2:20105400-20130200	Weak transcription	Lung	lung
14	chr2:20108600-20127400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr2:20108800-20137400	Weak transcription	Right Ventricle	heart
16	chr2:20111800-20127800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:20112200-20128400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:20112200-20130000	Weak transcription	HSMMtube	muscle
19	chr2:20112400-20128000	Weak transcription	Osteobl	bone
20	chr2:20112400-20128400	Weak transcription	NHDF-Ad	bronchial
21	chr2:20112600-20128800	Weak transcription	Hela-S3	cervix
22	chr2:20114000-20129000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr2:20114200-20128200	Weak transcription	HepG2	liver
24	chr2:20114400-20127400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr2:20114400-20143800	Weak transcription	Brain Substantia Nigra	brain
26	chr2:20116400-20127400	Weak transcription	Ovary	ovary
27	chr2:20116400-20128800	Weak transcription	A549	lung
28	chr2:20116600-20127400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:20116800-20127600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:20116800-20128600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr2:20117000-20127600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr2:20117000-20129000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr2:20117600-20188400	Weak transcription	Brain Angular Gyrus	brain
34	chr2:20121600-20127600	Weak transcription	Colon Smooth Muscle	Colon
35	chr2:20121600-20130600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr2:20121600-20135800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr2:20122600-20127400	Weak transcription	Fetal Brain Female	brain
38	chr2:20122800-20130600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr2:20123000-20127400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:20123400-20135800	Weak transcription	Brain Hippocampus Middle	brain
41	chr2:20124000-20127800	Weak transcription	Fetal Stomach	stomach
42	chr2:20124200-20128000	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr2:20124400-20130600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:20124800-20127600	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr2:20124800-20142800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
46	chr2:20125000-20127600	Weak transcription	Left Ventricle	heart
47	chr2:20125000-20127600	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr2:20125200-20129000	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr2:20125200-20129000	Weak transcription	HUVEC	blood vessel
50	chr2:20125200-20132800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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