Variant report

Variant	rs6802817
Chromosome Location	chr3:99779264-99779265
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:99594318..99596497-chr3:99778604..99780879,2	K562	blood:

Variant related genes	Relation type
ENSG00000168386	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10222474	0.86[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10936008	0.82[TSI][hapmap]
rs11719468	0.84[CEU][hapmap];0.94[JPT][hapmap]
rs12488245	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13059754	0.83[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap]
rs1384062	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs1387647	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16841874	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs1718235	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs2130369	0.88[CEU][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs35422475	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4577503	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap]
rs4928150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap]
rs4928151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4928153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4928230	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs4928235	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4928237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6440967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6767441	0.92[CEU][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6798114	0.84[CEU][hapmap]
rs6806323	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6808765	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7619512	0.80[ASN][1000 genomes]
rs7629487	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7636776	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7638900	0.82[TSI][hapmap]
rs7649349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7650727	0.84[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap]
rs766778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs793439	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs793440	0.82[TSI][hapmap]
rs793464	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap]
rs793502	0.83[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs793503	0.82[TSI][hapmap]
rs796976	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs813218	0.84[CEU][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs902159	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs923472	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9289981	0.87[CEU][hapmap]
rs9811920	0.92[CEU][hapmap];0.82[GIH][hapmap];0.84[MEX][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9814549	0.84[CEU][hapmap]
rs9837131	0.92[CEU][hapmap];0.80[GIH][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9849632	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv817478	chr3:99474086-99955548	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv869848	chr3:99652246-99904276	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
4	nsv932634	chr3:99660690-99888854	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010579	chr3:99660754-99901817	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1008483	chr3:99660754-99903769	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1010897	chr3:99660754-99904783	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
8	nsv1001529	chr3:99661758-99892654	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
9	nsv536665	chr3:99661758-99892654	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
10	nsv591148	chr3:99774720-99905803	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6802817	OR5H6	cis	cerebellum	SCAN
rs6802817	C3orf26	Cis_1M	lymphoblastoid	RTeQTL
rs6802817	EPHX1	trans	cerebellum	SCAN
rs6802817	SENP7	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99713600-99787800	Weak transcription	Primary T cells from cord blood	blood
2	chr3:99767400-99779600	Weak transcription	Left Ventricle	heart
3	chr3:99767600-99779400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr3:99767600-99801000	Weak transcription	HSMM	muscle
5	chr3:99768200-99780400	Weak transcription	GM12878-XiMat	blood
6	chr3:99768400-99788000	Weak transcription	Primary B cells from cord blood	blood
7	chr3:99770800-99787600	Weak transcription	Fetal Muscle Leg	muscle
8	chr3:99774000-99794800	Weak transcription	Stomach Mucosa	stomach
9	chr3:99775000-99785800	Weak transcription	Fetal Intestine Small	intestine
10	chr3:99777400-99781600	Weak transcription	NHLF	lung
11	chr3:99777400-99782800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr3:99777400-99782800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr3:99777400-99787800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:99777600-99780000	Weak transcription	HepG2	liver
15	chr3:99777600-99782800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:99777800-99782600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:99778000-99780200	Enhancers	Aorta	Aorta
18	chr3:99778200-99779800	Enhancers	Ovary	ovary
19	chr3:99778400-99780800	Enhancers	K562	blood
20	chr3:99778400-99782800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:99778600-99784000	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr3:99778600-99787800	Weak transcription	Right Atrium	heart
23	chr3:99778800-99782600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr3:99779000-99779400	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:99779000-99780200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
26	chr3:99779000-99782800	Weak transcription	Osteobl	bone
27	chr3:99779200-99779600	Weak transcription	Psoas Muscle	Psoas
28	chr3:99779200-99780000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:99779200-99780200	Enhancers	Primary T cells fromperipheralblood	blood
30	chr3:99779200-99780400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr3:99779200-99780800	Enhancers	Monocytes-CD14+_RO01746	blood

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