Variant report

Variant	rs2948655
Chromosome Location	chr8:3769902-3769903
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10107710	0.81[JPT][hapmap]
rs10216531	0.81[JPT][hapmap]
rs11775224	0.81[JPT][hapmap]
rs11786370	0.81[JPT][hapmap]
rs1464619	0.90[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap]
rs1523259	0.82[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap]
rs1582765	0.91[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.81[ASN][1000 genomes]
rs1582766	0.85[CHB][hapmap];0.87[CHD][hapmap];0.84[JPT][hapmap];0.83[ASN][1000 genomes]
rs1829859	0.90[CHB][hapmap];0.82[JPT][hapmap]
rs1968322	0.90[CHB][hapmap];0.84[JPT][hapmap]
rs2177329	0.81[CHB][hapmap]
rs2554702	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs2627414	0.80[ASN][1000 genomes]
rs2627425	0.91[CHB][hapmap];0.92[CHD][hapmap]
rs2688286	1.00[CHB][hapmap];0.84[CHD][hapmap];0.89[JPT][hapmap]
rs2688291	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2688319	0.80[ASN][1000 genomes]
rs2688325	0.82[CHB][hapmap];0.86[CHD][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2688326	0.80[ASN][1000 genomes]
rs2688327	0.85[JPT][hapmap]
rs2912285	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2912288	0.85[CHB][hapmap];0.93[CHD][hapmap];0.84[JPT][hapmap]
rs2912295	0.83[JPT][hapmap]
rs2930370	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2930371	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2930372	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs2930373	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs2930377	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.86[TSI][hapmap]
rs2930378	0.95[CHB][hapmap];0.97[CHD][hapmap];0.84[JPT][hapmap];0.86[TSI][hapmap]
rs2948646	0.81[CHB][hapmap]
rs2948651	0.90[CHB][hapmap];0.89[JPT][hapmap]
rs2948652	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs2948660	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.90[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap]
rs2954611	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs2954612	0.91[CHB][hapmap];0.89[JPT][hapmap]
rs2954623	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2954624	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs2954625	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs2954626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2954628	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs2975324	0.86[CHB][hapmap];0.83[JPT][hapmap]
rs2975325	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs2975330	0.88[CHB][hapmap]
rs2975331	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2975332	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap]
rs2975333	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs4875797	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs8180892	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034076	chr8:3168033-3989947	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv539351	chr8:3168033-3989947	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1017164	chr8:3174168-4026811	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv539352	chr8:3174168-4026811	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1018218	chr8:3180287-4089011	Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1025204	chr8:3542586-3889592	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv539356	chr8:3542586-3889592	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
8	nsv949269	chr8:3556145-4246903	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv498034	chr8:3559289-3846288	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv889904	chr8:3580368-3786543	Enhancers Bivalent Enhancer Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv1034837	chr8:3623613-3880459	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv932135	chr8:3636535-3909039	ZNF genes & repeats Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv609750	chr8:3663971-3790254	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv1018306	chr8:3667329-3843087	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv889906	chr8:3674674-3811706	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv889907	chr8:3674674-3814493	Bivalent Enhancer ZNF genes & repeats Enhancers Active TSS Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
17	nsv889908	chr8:3674674-3816121	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
18	nsv889909	chr8:3674674-3817191	Enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv889910	chr8:3675634-3786543	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv1028411	chr8:3681898-3770783	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv539363	chr8:3681898-3770783	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
22	nsv1020335	chr8:3692864-3796281	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
23	nsv1022617	chr8:3701501-3770783	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer	n/a	n/a	inside rSNPs	diseases
24	nsv530863	chr8:3710810-4381378	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
25	nsv889912	chr8:3742354-3832731	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv889913	chr8:3747899-3832731	Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
27	nsv1016688	chr8:3754417-4003761	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
28	nsv539364	chr8:3754417-4003761	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
29	nsv1018362	chr8:3763280-3811123	Weak transcription Enhancers ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
30	nsv1027153	chr8:3769850-3790094	Enhancers	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2948655	CSMD1	cis	parietal	SCAN

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

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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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