Variant report

Variant	rs828599
Chromosome Location	chr3:98466222-98466223
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10470451	0.82[ASN][1000 genomes]
rs115931	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11923134	0.87[ASN][1000 genomes]
rs13315676	0.84[ASN][1000 genomes]
rs1440158	0.86[CHB][hapmap]
rs1530655	0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs278363	0.92[CEU][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs278370	1.00[ASW][hapmap];0.85[CEU][hapmap];0.82[GIH][hapmap];0.91[LWK][hapmap];0.87[MEX][hapmap];0.96[MKK][hapmap];0.83[TSI][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs278373	1.00[ASW][hapmap];0.92[CEU][hapmap];0.82[CHD][hapmap];0.91[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.98[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap]
rs278374	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28553326	0.86[ASN][1000 genomes]
rs28707457	0.86[ASN][1000 genomes]
rs3755569	0.87[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs3755570	0.85[ASN][1000 genomes]
rs3772091	0.83[ASN][1000 genomes]
rs3821358	0.87[CHB][hapmap];0.86[CHD][hapmap];0.83[ASN][1000 genomes]
rs4638909	0.83[ASN][1000 genomes]
rs56976804	0.86[ASN][1000 genomes]
rs60464352	0.84[ASN][1000 genomes]
rs62278471	0.86[ASN][1000 genomes]
rs7611040	0.87[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs7614161	0.86[ASN][1000 genomes]
rs7634817	0.82[MEX][hapmap]
rs7643537	0.83[ASN][1000 genomes]
rs828589	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs828593	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs828594	1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs828595	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.80[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828596	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828597	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828598	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs828602	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs828613	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs844159	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs844161	0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs865474	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs893831	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs893832	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9879927	0.91[CHB][hapmap];0.86[JPT][hapmap];0.86[ASN][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	esv3390386	chr3:98174549-98579953	Genic enhancers Strong transcription Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv591065	chr3:98204198-98766326	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1007140	chr3:98421229-99202458	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription 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	17 gene(s)	inside rSNPs	diseases
4	nsv536663	chr3:98421229-99202458	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv470783	chr3:98431225-98466222	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv877214	chr3:98445324-98738006	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 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	chr3:98453400-98468600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:98453400-98469400	Weak transcription	Aorta	Aorta
3	chr3:98454400-98478000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr3:98456600-98479600	Weak transcription	Dnd41	blood
5	chr3:98456800-98469800	Weak transcription	Thymus	Thymus
6	chr3:98457400-98467800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:98457800-98474400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:98458400-98474800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:98459000-98467200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr3:98459400-98469400	Weak transcription	Pancreas	Pancrea
11	chr3:98460600-98467000	Weak transcription	Psoas Muscle	Psoas
12	chr3:98460600-98467800	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:98462800-98467200	Enhancers	HepG2	liver
14	chr3:98462800-98467400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:98463400-98469400	Weak transcription	Right Atrium	heart
16	chr3:98463400-98481600	Weak transcription	Right Ventricle	heart
17	chr3:98463600-98469000	Weak transcription	HMEC	breast
18	chr3:98463600-98469200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr3:98463800-98477400	Weak transcription	Brain Substantia Nigra	brain
20	chr3:98464200-98467400	Weak transcription	Left Ventricle	heart
21	chr3:98464800-98466800	Enhancers	HUVEC	blood vessel
22	chr3:98464800-98467000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:98465000-98468600	Weak transcription	Liver	Liver
24	chr3:98465000-98470600	Enhancers	GM12878-XiMat	blood
25	chr3:98466000-98467600	Weak transcription	Gastric	stomach
26	chr3:98466200-98469600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr3:98466200-98469800	Enhancers	Fetal Heart	heart

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