Variant report

Variant	rs17366680
Chromosome Location	chr3:59900871-59900872
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11715245	0.83[LWK][hapmap];0.92[YRI][hapmap]
rs17061377	1.00[ASN][1000 genomes]
rs17366548	0.86[YRI][hapmap]
rs35510391	0.83[AFR][1000 genomes]
rs55658297	1.00[ASN][1000 genomes]
rs7349527	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636381	1.00[ASN][1000 genomes]
rs9681598	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428085	chr3:59782509-60070116	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv460564	chr3:59821071-59927727	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv590384	chr3:59821071-59927727	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv590386	chr3:59846067-59912377	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1002104	chr3:59875996-59907597	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	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
7	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17366680	DNAH12	cis	parietal	SCAN
rs17366680	FLNB	cis	parietal	SCAN
rs17366680	THOC7	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59873200-59904200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr3:59890600-59903600	Weak transcription	Fetal Thymus	thymus
3	chr3:59893000-59915800	Weak transcription	Thymus	Thymus
4	chr3:59894400-59902600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr3:59894400-59903200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr3:59896800-59902600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:59898200-59903600	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr3:59899400-59902600	Strong transcription	Primary T cells from cord blood	blood
9	chr3:59899600-59915800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:59900800-59901400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
11	chr3:59900800-59901800	Strong transcription	Dnd41	blood

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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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