Variant report

Variant	rs6758766
Chromosome Location	chr2:177630608-177630609
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10930752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11889984	1.00[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12467333	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12469087	0.83[CEU][hapmap];0.82[CHB][hapmap];0.81[MEX][hapmap];0.94[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12611718	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs12618099	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs1554824	0.82[ASN][1000 genomes]
rs2221939	0.83[CEU][hapmap]
rs4021394	0.94[CEU][hapmap];0.82[CHB][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4600700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4894197	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4894198	0.82[CHB][hapmap];0.95[CHD][hapmap];0.81[ASN][1000 genomes]
rs4894200	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6706063	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs6706426	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6714936	0.81[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527737	chr2:177538266-177692572	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv583686	chr2:177538266-177692572	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1006500	chr2:177548521-177707097	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv524841	chr2:177628258-177632714	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6758766	LOC100130691	cis	parietal	SCAN
rs6758766	HOXD11	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:177623400-177634400	Weak transcription	Right Atrium	heart
2	chr2:177628400-177631000	Enhancers	H9 Cell Line	embryonic stem cell
3	chr2:177628600-177631200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:177628800-177630800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr2:177628800-177631400	Enhancers	ES-I3 Cell Line	embryonic stem cell
6	chr2:177628800-177655400	Weak transcription	Ovary	ovary
7	chr2:177629000-177630800	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr2:177629200-177630800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr2:177629200-177631000	Enhancers	H1 Cell Line	embryonic stem cell
10	chr2:177629200-177633400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:177629400-177631000	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr2:177629600-177631200	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr2:177629600-177631400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr2:177630200-177631000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:177630400-177630800	Weak transcription	Primary B cells from peripheral blood	blood
16	chr2:177630600-177632800	Weak transcription	Gastric	stomach
17	chr2:177630600-177634000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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