Variant report

Variant	rs12122753
Chromosome Location	chr1:179340775-179340776
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179333622..179336435-chr1:179340051..179341753,2	K562	blood:
2	chr1:179332952..179336574-chr1:179337996..179342859,7	MCF-7	breast:
3	chr1:179334935..179337795-chr1:179340051..179343667,3	K562	blood:
4	chr1:179333390..179336673-chr1:179338029..179341473,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000162779	Chromatin interaction
ENSG00000263633	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1060775	1.00[JPT][hapmap]
rs10753193	0.91[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10798672	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798678	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10798682	1.00[JPT][hapmap]
rs10913763	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10913776	0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs10913804	1.00[JPT][hapmap]
rs10913807	1.00[JPT][hapmap]
rs12131398	1.00[JPT][hapmap]
rs12131400	1.00[JPT][hapmap]
rs12136100	1.00[JPT][hapmap]
rs1328596	1.00[JPT][hapmap]
rs1410590	1.00[JPT][hapmap]
rs1831180	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs1928004	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs4255343	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4297245	0.85[GIH][hapmap]
rs4360482	0.91[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap]
rs4421551	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4584358	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4606280	1.00[ASW][hapmap];0.91[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.92[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]
rs4625242	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4652386	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4652404	1.00[JPT][hapmap]
rs6659294	0.91[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap]
rs6662859	0.90[CEU][hapmap];0.85[CHB][hapmap];0.94[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6696896	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs6697280	0.90[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6697285	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6697373	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6698201	1.00[JPT][hapmap]
rs7512551	0.82[GIH][hapmap];1.00[JPT][hapmap]
rs7514278	0.88[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.82[TSI][hapmap]
rs7518843	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7522064	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7529133	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7535603	0.80[CEU][hapmap]
rs7540732	0.85[CEU][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7541905	0.93[GIH][hapmap]
rs7542099	0.82[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs928016	1.00[JPT][hapmap]
rs963062	1.00[JPT][hapmap]
rs964982	0.82[GIH][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv33901	chr1:179328708-179344905	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12122753	TDRD5	cis	parietal	SCAN
rs12122753	SNORD80	cis	parietal	SCAN

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

No data

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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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