Variant report

Variant	rs6807838
Chromosome Location	chr3:118688424-118688425
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1158699	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485923	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492855	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435655	1.00[CEU][hapmap];0.94[MEX][hapmap]
rs16829179	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2160054	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28484956	0.82[AFR][1000 genomes]
rs28565574	0.85[AFR][1000 genomes]
rs28573387	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28592657	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655404	0.82[AFR][1000 genomes]
rs3821882	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4611809	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56728928	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58284747	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772441	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773865	1.00[CEU][hapmap];0.94[MEX][hapmap]
rs6779428	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6795721	0.87[ASW][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs6796798	0.84[MKK][hapmap]
rs6807110	1.00[CEU][hapmap];0.94[MEX][hapmap]
rs72966895	0.83[AFR][1000 genomes]
rs72968605	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72968610	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72968613	0.85[AFR][1000 genomes]
rs72968638	0.86[AFR][1000 genomes]
rs7633584	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811829	0.86[AFR][1000 genomes]
rs9817943	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821022	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9821458	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826100	0.82[YRI][hapmap]
rs9828087	0.85[AFR][1000 genomes]
rs9828870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833229	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836642	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849421	0.85[AFR][1000 genomes]
rs9855713	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860140	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867214	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873807	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874208	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9874337	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv1010475	chr3:118657382-118789714	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv877369	chr3:118681771-118824418	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118681200-118694000	Enhancers	Brain Substantia Nigra	brain
2	chr3:118681400-118690000	Enhancers	Brain Hippocampus Middle	brain
3	chr3:118681800-118692800	Enhancers	Brain Anterior Caudate	brain
4	chr3:118683400-118696200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:118683800-118689000	Enhancers	iPS-18 Cell Line	embryonic stem cell
6	chr3:118684400-118690000	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr3:118684600-118690200	Enhancers	Brain Cingulate Gyrus	brain
8	chr3:118684800-118690200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr3:118684800-118694000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr3:118685000-118688800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:118685000-118690000	Enhancers	Brain Angular Gyrus	brain
12	chr3:118685400-118689400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
13	chr3:118686200-118689000	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr3:118686600-118690200	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr3:118687000-118690000	Enhancers	Stomach Smooth Muscle	stomach
16	chr3:118687200-118690200	Enhancers	Fetal Heart	heart
17	chr3:118687400-118691800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr3:118687400-118691800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:118687600-118689000	Enhancers	H1 Cell Line	embryonic stem cell
20	chr3:118687800-118688800	Enhancers	Right Atrium	heart
21	chr3:118687800-118690400	Enhancers	Brain Germinal Matrix	brain
22	chr3:118688200-118689000	Enhancers	Ovary	ovary
23	chr3:118688200-118689000	Enhancers	Psoas Muscle	Psoas
24	chr3:118688200-118689200	Enhancers	Left Ventricle	heart
25	chr3:118688200-118689400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr3:118688400-118688600	Enhancers	Rectal Smooth Muscle	rectum
27	chr3:118688400-118689000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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