Variant report

Variant	rs2670908
Chromosome Location	chr11:64737052-64737053
allele	C/T
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]
rs11231913	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs17146441	0.84[TSI][hapmap]
rs2285346	0.84[CEU][hapmap];0.86[CHB][hapmap];0.84[TSI][hapmap];0.88[YRI][hapmap]
rs240565	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240567	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs240571	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs240572	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2518909	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35131180	0.81[EUR][1000 genomes]
rs470511	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs519796	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs574381	0.87[CHB][hapmap]
rs594392	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs610130	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs618006	0.87[CHB][hapmap]
rs626670	0.83[GIH][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap]
rs673995	0.87[ASW][hapmap];0.81[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.94[MKK][hapmap];0.88[YRI][hapmap]
rs675090	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs688749	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1539 gene(s)	inside rSNPs	diseases
2	nsv555208	chr11:64645119-64771179	Weak transcription Active TSS Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1029 gene(s)	inside rSNPs	diseases
3	nsv976460	chr11:64727780-64743097	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2670908	SPDYC	cis	Whole Blood	GTEx

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64730200-64738400	Weak transcription	Stomach Mucosa	stomach
2	chr11:64735200-64739000	Weak transcription	GM12878-XiMat	blood
3	chr11:64736000-64739000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr11:64736200-64738400	Enhancers	NHEK	skin
5	chr11:64736200-64739000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr11:64736400-64737800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:64736400-64739200	Enhancers	HMEC	breast
8	chr11:64736600-64737600	Enhancers	HUVEC	blood vessel
9	chr11:64736600-64737800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr11:64736800-64737400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr11:64737000-64737200	Enhancers	Brain Cingulate Gyrus	brain
12	chr11:64737000-64737200	Enhancers	Fetal Intestine Small	intestine
13	chr11:64737000-64737200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
14	chr11:64737000-64737200	Enhancers	NH-A	brain
15	chr11:64737000-64737400	Enhancers	Placenta	Placenta
16	chr11:64737000-64737400	Enhancers	Rectal Mucosa Donor 31	rectum

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Input of quick search could be:

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

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