Variant report

Variant	rs943964
Chromosome Location	chr1:104668220-104668221
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AMY1C-2	chr1:104668179-104668541	XLOC_000326
2	lnc-AMY1C-2	chr1:104668178-104668541	NONHSAT004905

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10449725	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11576074	1.00[ASN][1000 genomes]
rs11577070	1.00[ASN][1000 genomes]
rs11583722	1.00[ASN][1000 genomes]
rs1928301	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928302	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1928315	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs1932473	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28405193	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57106041	1.00[EUR][1000 genomes]
rs59789357	1.00[EUR][1000 genomes]
rs6671467	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6679346	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72685703	1.00[ASN][1000 genomes]
rs72685776	1.00[ASN][1000 genomes]
rs72685792	1.00[ASN][1000 genomes]
rs72685793	1.00[ASN][1000 genomes]
rs72685796	1.00[ASN][1000 genomes]
rs72689166	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689167	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689174	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689176	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689177	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689180	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689182	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689183	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689185	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689186	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs72689187	0.98[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs943962	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014507	chr1:104307231-104784753	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1012931	chr1:104322484-104778961	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv872072	chr1:104470622-105076810	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1010903	chr1:104483363-105468941	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv872073	chr1:104502333-104719055	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv1005132	chr1:104546037-104675264	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	esv1834182	chr1:104576359-104672830	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	esv1839044	chr1:104576359-104707906	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv482341	chr1:104589525-104731812	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv1842590	chr1:104640211-104672052	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
11	esv1835672	chr1:104659907-104670141	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
12	esv1839868	chr1:104659907-104672830	Enhancers Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
13	esv3519315	chr1:104668122-104670754	Enhancers Weak transcription	lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:104667800-104669000	Enhancers	Primary hematopoietic stem cells	blood
2	chr1:104667800-104669000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr1:104667800-104669200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:104668000-104668400	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr1:104668000-104668400	Enhancers	Placenta Amnion	Placenta Amnion
6	chr1:104668000-104669400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr1:104668200-104668800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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