Variant report

Variant	rs6774929
Chromosome Location	chr3:21480184-21480185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:21475881..21478303-chr3:21479412..21482583,3	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs12638887	0.81[CHB][hapmap]
rs13061028	0.82[CHD][hapmap]
rs13069346	0.87[EUR][1000 genomes]
rs2076829	0.82[CHB][hapmap]
rs341850	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs341852	0.80[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs341853	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs341854	0.89[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs368255	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3732905	0.85[CEU][hapmap];0.89[CHB][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3821733	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3849537	1.00[CEU][hapmap];0.88[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3849539	0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3860572	0.85[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4389495	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4501133	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs453364	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4857999	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4858000	0.85[CEU][hapmap];0.94[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4858001	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4858002	0.85[CEU][hapmap];0.94[CHB][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4858321	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4858322	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6550607	0.80[CEU][hapmap];0.94[CHB][hapmap];0.82[MKK][hapmap];0.85[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6550608	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6787456	0.85[CEU][hapmap];0.94[CHB][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6787955	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6797692	0.85[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6806788	0.88[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7611710	0.84[CEU][hapmap];0.89[CHB][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7614523	0.88[CHB][hapmap];0.88[CHD][hapmap];0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs7625365	0.84[CEU][hapmap];0.89[CHB][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7634661	0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7643842	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9809197	0.84[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9838377	0.86[ASN][1000 genomes]
rs9859442	0.87[EUR][1000 genomes]
rs9874351	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879872	0.82[CHB][hapmap];0.82[CHD][hapmap]
rs9883841	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834630	chr3:21311619-21491327	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1006471	chr3:21385627-21596955	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv534005	chr3:21387588-22003293	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1000828	chr3:21399870-21565580	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv536515	chr3:21399870-21565580	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6774929	NR1D2	cis	parietal	SCAN
rs6774929	ZNF385D	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:21458800-21483400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:21463000-21491400	Weak transcription	Aorta	Aorta
3	chr3:21477000-21491200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:21477000-21507200	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:21477400-21488600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:21477800-21487600	Weak transcription	Fetal Stomach	stomach
7	chr3:21478400-21488400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:21478800-21481800	Weak transcription	Fetal Kidney	kidney
9	chr3:21478800-21488600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr3:21479000-21484400	Weak transcription	Left Ventricle	heart
11	chr3:21479400-21480200	Enhancers	Fetal Heart	heart
12	chr3:21480000-21480200	Enhancers	Fetal Lung	lung
13	chr3:21480000-21489000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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