Variant report

Variant	rs482337
Chromosome Location	chr20:24192721-24192722
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYNDIG1-2	chr20:24191985-24193327	XLOC_013497

Extended variants
information (count: 71 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs112837	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs224153	0.80[ASN][1000 genomes]
rs224154	0.82[ASN][1000 genomes]
rs2474441	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2644845	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2644846	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2748885	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2749424	0.81[ASN][1000 genomes]
rs2749425	0.93[ASN][1000 genomes]
rs2749427	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2749459	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34536107	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs472526	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs473253	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485747	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs492884	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs494639	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501262	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502250	0.98[ASN][1000 genomes]
rs504500	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504964	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs512615	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs512754	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs513654	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs523233	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs525009	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs527873	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs529793	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs530523	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs530525	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs530615	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs531361	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs545266	0.97[ASN][1000 genomes]
rs546094	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs546946	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs547449	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs550792	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs562594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs563102	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs564245	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs564337	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565074	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs565833	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs566047	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566089	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs569066	0.97[ASN][1000 genomes]
rs570480	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs572702	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs573964	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs576373	0.81[ASN][1000 genomes]
rs6049501	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049502	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6049503	0.97[ASN][1000 genomes]
rs6049504	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6138237	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs85687	0.81[ASN][1000 genomes]
rs85689	0.81[ASN][1000 genomes]
rs858060	0.83[ASN][1000 genomes]
rs858061	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs858066	0.83[ASN][1000 genomes]
rs858067	0.83[ASN][1000 genomes]
rs858068	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs858069	0.84[ASN][1000 genomes]
rs858070	0.84[ASN][1000 genomes]
rs858071	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs858072	0.95[ASN][1000 genomes]
rs858074	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs858075	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3328348	chr20:24095746-24285830	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv833945	chr20:24163437-24349462	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24189600-24193200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr20:24190400-24196000	Enhancers	Fetal Intestine Large	intestine
3	chr20:24190800-24192800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr20:24191800-24194200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
5	chr20:24192000-24193000	Bivalent Enhancer	Fetal Thymus	thymus
6	chr20:24192000-24195600	Enhancers	Fetal Intestine Small	intestine
7	chr20:24192200-24193000	Enhancers	iPS-18 Cell Line	embryonic stem cell
8	chr20:24192200-24193600	Enhancers	Placenta Amnion	Placenta Amnion
9	chr20:24192200-24193800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr20:24192200-24193800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr20:24192200-24194000	Enhancers	H1 Cell Line	embryonic stem cell
12	chr20:24192200-24194000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr20:24192200-24194000	Enhancers	HUES64 Cell Line	embryonic stem cell
14	chr20:24192400-24192800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr20:24192400-24193000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr20:24192400-24193200	Enhancers	Primary hematopoietic stem cells	blood
17	chr20:24192400-24194000	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr20:24192600-24192800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr20:24192600-24192800	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr20:24192600-24192800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr20:24192600-24193000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr20:24192600-24193200	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr20:24192600-24194000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr20:24192600-24194000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr20:24192600-24194200	Enhancers	iPS-15b Cell Line	embryonic stem cell

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