Variant report

Variant	rs6706340
Chromosome Location	chr2:99369845-99369846
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10177696	0.82[EUR][1000 genomes]
rs10194177	0.81[EUR][1000 genomes]
rs10196218	0.84[CHB][hapmap];0.84[CHD][hapmap]
rs10199267	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10460485	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12477450	0.82[EUR][1000 genomes]
rs12622931	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13391794	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13410406	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13428808	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1514916	0.82[EUR][1000 genomes]
rs41445250	0.82[EUR][1000 genomes]
rs58666702	0.82[EUR][1000 genomes]
rs60024860	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6733957	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6737760	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6751196	0.81[EUR][1000 genomes]
rs7577636	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7601040	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv1011278	chr2:99280928-99638376	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535835	chr2:99280928-99638376	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv520854	chr2:99369757-99373720	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6706340	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99359600-99374000	Weak transcription	Aorta	Aorta
2	chr2:99361400-99374000	Weak transcription	Pancreas	Pancrea
3	chr2:99362400-99372800	Weak transcription	Primary T cells from cord blood	blood
4	chr2:99364800-99371200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr2:99365200-99372200	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:99365400-99371600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:99365400-99372400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr2:99365600-99373600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr2:99365800-99374400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:99366200-99372200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr2:99366600-99373200	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr2:99367000-99370200	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr2:99367200-99370000	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr2:99367400-99374000	Weak transcription	Esophagus	oesophagus
15	chr2:99368800-99370000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr2:99369600-99373600	Weak transcription	HUVEC	blood vessel
17	chr2:99369800-99371200	Enhancers	Primary neutrophils fromperipheralblood	blood

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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