Variant report

Variant	rs6683623
Chromosome Location	chr1:179407408-179407409
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1060775	0.80[GIH][hapmap]
rs10798671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10913764	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913776	0.81[GIH][hapmap]
rs10913801	0.85[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs10913805	0.84[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs11580135	0.94[CEU][hapmap]
rs12743373	0.89[MKK][hapmap]
rs12757065	0.89[MKK][hapmap]
rs1329277	0.89[ASN][1000 genomes]
rs1410590	0.80[GIH][hapmap]
rs1590784	0.92[ASN][1000 genomes]
rs1590786	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1831180	0.84[GIH][hapmap]
rs1928004	0.84[GIH][hapmap]
rs3898486	0.85[CHB][hapmap];0.85[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.89[ASN][1000 genomes]
rs4268319	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4297245	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.85[MEX][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap]
rs4360482	0.92[GIH][hapmap]
rs4442334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs4504843	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4606280	0.80[GIH][hapmap]
rs4625243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4651025	0.92[MKK][hapmap]
rs4651038	0.85[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4652374	0.92[MKK][hapmap]
rs4652382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6425558	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659294	0.92[GIH][hapmap]
rs6662859	0.92[GIH][hapmap]
rs6664339	0.95[MKK][hapmap]
rs6678667	0.92[MKK][hapmap]
rs6696896	0.84[GIH][hapmap]
rs6702905	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7512551	0.84[GIH][hapmap]
rs7514278	0.81[GIH][hapmap]
rs7541905	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap]
rs928016	0.80[GIH][hapmap]
rs964982	0.84[GIH][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	esv1819329	chr1:179371973-179442337	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv466217	chr1:179371973-179477921	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv548297	chr1:179371973-179477921	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv548298	chr1:179376896-179436288	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6683623	TDRD5	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179405200-179413000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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