Variant report

Variant	rs11760662
Chromosome Location	chr7:39297342-39297343
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10081326	0.95[CEU][hapmap];1.00[JPT][hapmap]
rs10085664	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11764181	0.82[CEU][hapmap]
rs4416740	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4446648	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.90[ASN][1000 genomes]
rs4563790	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4599718	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.90[ASN][1000 genomes]
rs4629763	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs4723833	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6462896	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6462899	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[ASN][1000 genomes]
rs6966337	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6967316	0.93[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.82[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9648476	0.90[ASN][1000 genomes]

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	nsv1024142	chr7:38978728-39300444	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1015572	chr7:39185895-39413053	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv538821	chr7:39185895-39413053	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv887969	chr7:39265429-39391875	Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11760662	TXNDC3	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:39288800-39298000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr7:39288800-39298200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr7:39292800-39298000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr7:39293000-39298000	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr7:39293000-39298200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr7:39293000-39298400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:39293000-39299800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr7:39293600-39298600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr7:39293800-39298200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr7:39293800-39310600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr7:39297000-39299200	Enhancers	HUES48 Cell Line	embryonic stem cell
12	chr7:39297200-39297400	Enhancers	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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