Variant report

Variant	rs4297245
Chromosome Location	chr1:179361178-179361179
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10753193	0.85[GIH][hapmap]
rs10798671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10913764	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10913801	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap]
rs10913805	0.84[CHB][hapmap];0.88[JPT][hapmap];0.81[ASN][1000 genomes]
rs11580135	0.94[CEU][hapmap]
rs12122753	0.85[GIH][hapmap]
rs12743373	0.88[MKK][hapmap]
rs12757065	0.88[MKK][hapmap]
rs1329277	0.81[ASN][1000 genomes]
rs1590786	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1831180	0.82[GIH][hapmap]
rs1928004	0.82[GIH][hapmap]
rs3898486	0.85[CHB][hapmap];0.85[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.81[ASN][1000 genomes]
rs4268319	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4360482	0.82[GIH][hapmap]
rs4442334	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4504843	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4606280	0.92[GIH][hapmap]
rs4625243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4651025	0.85[MKK][hapmap]
rs4651038	0.85[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4652374	0.85[MKK][hapmap]
rs4652382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6425558	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6659294	0.82[GIH][hapmap]
rs6662859	0.82[GIH][hapmap]
rs6664339	0.86[MKK][hapmap]
rs6678667	0.85[MKK][hapmap]
rs6683623	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];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6696896	0.82[GIH][hapmap]
rs6702905	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7512551	0.82[GIH][hapmap]
rs7541905	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs964982	0.82[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005278	chr1:179197645-179371395	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	16 gene(s)	inside rSNPs	diseases
2	esv2762031	chr1:179323738-179375197	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
3	nsv518403	chr1:179323919-179371973	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
4	nsv548279	chr1:179323919-179390148	Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3514400	chr1:179349344-179400533	Enhancers Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv3514401	chr1:179349344-179400533	Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3451112	chr1:179352344-179400533	Enhancers ZNF genes & repeats Weak transcription Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv523087	chr1:179352736-179371973	ZNF genes & repeats Enhancers Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4297245	TDRD5	cis	parietal	SCAN
rs4297245	TDRD5	cis	intralobular white matter	BrainEAC

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
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