Variant report

Variant	rs6548978
Chromosome Location	chr3:68139530-68139531
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10865603	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11921557	0.93[ASN][1000 genomes]
rs13078759	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs1595489	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4302389	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4419383	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs4508789	1.00[CEU][hapmap]
rs4602395	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs56831191	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57701717	0.91[ASN][1000 genomes]
rs60993082	0.93[ASN][1000 genomes]
rs6548943	1.00[CEU][hapmap];0.88[CHB][hapmap];0.80[EUR][1000 genomes]
rs6548957	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6548958	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6548964	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6548970	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6548977	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6548979	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6548992	0.82[CEU][hapmap]
rs6549006	1.00[CEU][hapmap]
rs6549018	0.93[ASN][1000 genomes]
rs6771439	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs6777162	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6781199	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6785163	1.00[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6786795	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6792628	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6809593	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7626911	0.93[ASN][1000 genomes]
rs7630992	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs7634100	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs9309966	0.82[CEU][hapmap]
rs961915	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap]
rs9860971	0.89[ASN][1000 genomes]
rs9867112	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9874375	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[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	nsv1002010	chr3:67785913-68312064	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1009871	chr3:67862617-68312064	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv536583	chr3:67862617-68312064	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv999747	chr3:68066423-68188180	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv536584	chr3:68066423-68188180	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	esv2752014	chr3:68091879-68416989	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1007450	chr3:68094416-68346546	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs6548978	SLC5A7	trans	brain	seeQTL
rs6548978	LRTM1	trans	brain	seeQTL
rs6548978	SPARC	trans	brain	seeQTL
rs6548978	PDE6H	trans	brain	seeQTL
rs6548978	DEFB119	trans	brain	seeQTL
rs6548978	TTR	trans	brain	seeQTL
rs6548978	ASMT	trans	brain	seeQTL
rs6548978	GUCA1C	trans	brain	seeQTL
rs6548978	LTF	trans	brain	seeQTL
rs6548978	SH2D2A	trans	brain	seeQTL
rs6548978	CRX	trans	brain	seeQTL

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:68134200-68140400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:68134400-68140200	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr3:68134400-68140400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:68134400-68140400	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:68134400-68141000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr3:68134600-68140400	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr3:68134600-68141000	Enhancers	Primary T cells from cord blood	blood
8	chr3:68135000-68140400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr3:68136000-68140000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr3:68137000-68140200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr3:68137400-68140000	Enhancers	Fetal Stomach	stomach
12	chr3:68138200-68139600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr3:68138600-68140000	Enhancers	Rectal Smooth Muscle	rectum
14	chr3:68138800-68140000	Enhancers	NH-A	brain
15	chr3:68139000-68140000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr3:68139200-68139800	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr3:68139200-68140000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr3:68139200-68140000	Enhancers	Aorta	Aorta
19	chr3:68139400-68139600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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