Variant report

Variant	rs6804301
Chromosome Location	chr3:60003650-60003651
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs212027	0.81[CEU][hapmap]
rs3856659	0.85[CHD][hapmap]
rs3912493	0.93[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.88[JPT][hapmap];0.80[MKK][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6782804	0.85[EUR][1000 genomes]
rs6794968	0.81[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.83[JPT][hapmap];0.83[EUR][1000 genomes]
rs7614540	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9819370	0.98[ASN][1000 genomes]
rs9825153	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6804301	CCDC66	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:59996800-60011600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:59997200-60005800	Enhancers	Primary T helper cells fromperipheralblood	blood
3	chr3:59999000-60005000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:60000800-60012600	Enhancers	Primary T killer memory cells from peripheral blood	blood
5	chr3:60001200-60004400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr3:60002000-60004800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr3:60002200-60004200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
8	chr3:60002200-60004400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr3:60002200-60005800	Enhancers	Primary T cells fromperipheralblood	blood
10	chr3:60002200-60005800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:60002400-60004400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:60002800-60004000	Enhancers	NHEK	skin
13	chr3:60002800-60004400	Flanking Active TSS	Dnd41	blood
14	chr3:60003000-60003800	Enhancers	Fetal Thymus	thymus
15	chr3:60003000-60003800	Enhancers	Thymus	Thymus
16	chr3:60003000-60004000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:60003000-60004000	Enhancers	HMEC	breast
18	chr3:60003000-60004200	ZNF genes & repeats	GM12878-XiMat	blood
19	chr3:60003000-60004200	Enhancers	NH-A	brain
20	chr3:60003000-60004400	Enhancers	Primary B cells from peripheral blood	blood
21	chr3:60003200-60003800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr3:60003400-60003800	Enhancers	Primary hematopoietic stem cells short term culture	blood
23	chr3:60003400-60004600	Enhancers	Fetal Heart	heart
24	chr3:60003600-60003800	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr3:60003600-60003800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr3:60003600-60009400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:60003600-60012800	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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