Variant report

Variant	rs9872356
Chromosome Location	chr3:60371053-60371054
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12637099	0.95[CEU][hapmap];0.82[CHB][hapmap];0.85[EUR][1000 genomes]
rs1380465	0.95[CEU][hapmap]
rs1380466	0.95[CEU][hapmap];0.82[GIH][hapmap]
rs17062892	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs17062963	0.95[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17062966	0.91[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs242171	0.86[CEU][hapmap]
rs2687165	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2687168	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2687169	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2687170	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2734363	0.82[CHB][hapmap]
rs2734380	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4615035	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6783454	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.85[EUR][1000 genomes]
rs6801889	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6807277	0.90[CEU][hapmap];0.82[EUR][1000 genomes]
rs6808129	0.95[CEU][hapmap];0.82[CHB][hapmap];0.82[EUR][1000 genomes]
rs72624872	0.94[EUR][1000 genomes]
rs73094220	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7618479	0.91[CEU][hapmap];0.81[CHD][hapmap];0.88[GIH][hapmap];0.89[MEX][hapmap];0.86[EUR][1000 genomes]
rs7646666	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9824749	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9835058	0.90[YRI][hapmap]
rs9836899	0.81[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9837246	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9841239	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9847570	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9847855	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9848065	0.91[CEU][hapmap];1.00[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs9862806	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9862809	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9867241	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9874387	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs9877008	0.95[CEU][hapmap];0.81[GIH][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1009971	chr3:60070974-60397331	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010969	chr3:60124962-60425297	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv590394	chr3:60289140-60388900	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv1011408	chr3:60307954-60417143	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv1011133	chr3:60309541-60417339	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv519353	chr3:60310790-60417103	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv460568	chr3:60310790-60417103	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv590395	chr3:60310790-60417103	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv1013291	chr3:60312356-60417339	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv590396	chr3:60330356-60447990	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv997531	chr3:60340440-60504992	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv876846	chr3:60347122-60382828	Active TSS Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv876847	chr3:60352975-60382828	Enhancers Weak transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv1010314	chr3:60367530-60459926	Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv876848	chr3:60367607-60420665	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv590397	chr3:60367607-60458976	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9872356	B4GALT2	trans	parietal	SCAN
rs9872356	CCDC66	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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