Variant report

Variant	rs6784057
Chromosome Location	chr3:59982993-59982994
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10490808	0.87[CEU][hapmap];0.86[GIH][hapmap];0.82[MKK][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs11130742	0.87[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs11130743	0.85[EUR][1000 genomes]
rs12630463	0.85[EUR][1000 genomes]
rs13061337	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13063413	1.00[ASW][hapmap];1.00[LWK][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs13073897	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13081936	0.87[CEU][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs13081972	0.83[EUR][1000 genomes]
rs13086424	0.82[CHB][hapmap];0.84[GIH][hapmap]
rs13088505	0.83[EUR][1000 genomes]
rs13088669	0.81[EUR][1000 genomes]
rs13092173	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs13092997	0.85[EUR][1000 genomes]
rs13094437	0.84[EUR][1000 genomes]
rs13096138	0.91[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs212014	0.90[CEU][hapmap];0.90[EUR][1000 genomes]
rs2736791	0.90[EUR][1000 genomes]
rs3772458	0.83[EUR][1000 genomes]
rs3772464	0.83[LWK][hapmap]
rs3772468	0.82[EUR][1000 genomes]
rs3772473	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs3772483	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs3772491	0.87[CEU][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs3772492	0.87[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs3772499	0.87[CEU][hapmap];0.83[CHB][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.91[AFR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3772500	0.87[CEU][hapmap];0.82[CHB][hapmap];0.87[TSI][hapmap];0.90[EUR][1000 genomes]
rs3772502	0.95[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs3772505	1.00[ASW][hapmap];0.95[CEU][hapmap];0.91[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3821478	0.82[EUR][1000 genomes]
rs3821479	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs3821481	0.87[CEU][hapmap];0.91[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs4679625	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6771484	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs7640107	0.87[CEU][hapmap];0.85[GIH][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
3	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
4	nsv876838	chr3:59952152-59999690	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv590388	chr3:59957252-60018326	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv590389	chr3:59981525-59998389	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6784057	CCDC66	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59967400-59993000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:59968000-59986600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr3:59972800-59983600	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr3:59974200-59983000	Enhancers	Fetal Thymus	thymus
5	chr3:59974400-59983000	Enhancers	Thymus	Thymus
6	chr3:59975200-59984000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr3:59976800-59984000	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr3:59977200-59983800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr3:59978200-59985000	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr3:59978400-59984600	Enhancers	Primary T cells from cord blood	blood
11	chr3:59978800-59983400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr3:59980600-59983200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:59980600-59992800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr3:59980800-59983800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr3:59980800-59983800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:59981000-59983400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:59981200-59983400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:59982000-59986000	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr3:59982600-59983000	Strong transcription	Dnd41	blood
20	chr3:59982600-59984400	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr3:59982800-59983400	Weak transcription	Fetal Lung	lung
22	chr3:59982800-59984200	Enhancers	HUES48 Cell Line	embryonic stem cell

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