Variant report

Variant	rs6446109
Chromosome Location	chr3:60076989-60076990
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 58 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs13060068	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17061972	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs17257269	1.00[CHB][hapmap]
rs212010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs212036	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs212038	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs2223085	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2361336	1.00[JPT][hapmap]
rs2361337	1.00[CEU][hapmap]
rs2366953	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2630165	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2630182	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2630195	1.00[ASN][1000 genomes]
rs2630205	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2736763	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2736776	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2736820	1.00[ASN][1000 genomes]
rs34267930	0.89[ASN][1000 genomes]
rs3845974	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4024129	1.00[JPT][hapmap]
rs4679629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679631	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679636	1.00[CEU][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs6446110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67136973	0.89[ASN][1000 genomes]
rs6773600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789112	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs6791450	1.00[JPT][hapmap]
rs6794055	1.00[JPT][hapmap]
rs6797474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6804216	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6806074	1.00[JPT][hapmap]
rs7609578	1.00[JPT][hapmap]
rs7642268	1.00[JPT][hapmap]
rs9311748	0.89[ASN][1000 genomes]
rs969562	1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9833389	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv834707	chr3:60005679-60184046	Weak transcription Enhancers Flanking Active TSS 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	1 gene(s)	inside rSNPs	diseases
4	esv2752010	chr3:60067396-60288428	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1009063	chr3:60067866-60277128	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1013919	chr3:60067866-60284882	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv519855	chr3:60068730-60276722	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv460566	chr3:60068730-60276722	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv460567	chr3:60068730-60276722	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv590390	chr3:60068730-60276722	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv590391	chr3:60068730-60277709	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1008586	chr3:60070974-60258108	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv536576	chr3:60070974-60258108	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	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
15	nsv1008267	chr3:60071947-60264461	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv1007798	chr3:60071947-60277128	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv2763751	chr3:60071959-60292312	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv2752011	chr3:60073153-60288428	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv432421	chr3:60073153-60288428	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6446109	MEF2A	trans	brain	seeQTL
rs6446109	SF1	trans	brain	seeQTL
rs6446109	AGAP4	trans	brain	seeQTL
rs6446109	SLC1A2	trans	brain	seeQTL
rs6446109	BBS5	trans	brain	seeQTL
rs6446109	CBX5	trans	brain	seeQTL
rs6446109	DGKG	trans	brain	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60073000-60080400	Weak transcription	Primary B cells from cord blood	blood
2	chr3:60075800-60077400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr3:60075800-60077400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr3:60075800-60077800	Enhancers	Fetal Thymus	thymus
5	chr3:60076000-60077000	Enhancers	Primary T helper naive cells from peripheral blood	blood
6	chr3:60076000-60077200	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr3:60076200-60077800	Enhancers	Primary T cells from cord blood	blood
8	chr3:60076400-60077400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr3:60076600-60077800	Enhancers	Thymus	Thymus
10	chr3:60076800-60077200	Enhancers	Primary T killer memory cells from peripheral blood	blood
11	chr3:60076800-60080200	Weak transcription	Dnd41	blood

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