Variant report

Variant	rs6468807
Chromosome Location	chr8:102988273-102988274
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10097554	0.84[CEU][hapmap]
rs10098273	0.90[EUR][1000 genomes]
rs10099842	0.92[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs10105502	0.89[YRI][hapmap]
rs1119377	1.00[ASW][hapmap];1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11778653	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs12545403	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs1371739	0.88[EUR][1000 genomes]
rs1371740	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs1543771	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17495818	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs1866690	0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1866691	0.96[CEU][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1866692	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1866693	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2023269	0.89[YRI][hapmap]
rs2119226	0.89[CEU][hapmap]
rs4145554	0.96[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs4734042	0.82[CEU][hapmap]
rs4734043	1.00[CEU][hapmap];0.80[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4734044	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734046	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4734602	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs4734603	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4734604	0.88[EUR][1000 genomes]
rs4734606	0.82[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4734607	0.89[YRI][hapmap]
rs6468803	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs6468804	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs6468805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6468806	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6981347	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6982001	0.94[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6991019	0.96[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs6991178	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs6995105	0.92[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs6999047	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6999316	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7003320	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7010848	0.96[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs7015981	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs7820244	0.92[CEU][hapmap];0.91[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs7823856	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7838556	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7838767	0.92[EUR][1000 genomes]
rs7839884	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs7840045	0.92[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs7841927	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs984928	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018653	chr8:102818271-103009082	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv539700	chr8:102818271-103009082	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv831411	chr8:102937991-103108140	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6468807	STK3	cis	cerebellum	SCAN
rs6468807	NCALD	cis	lymphoblastoid	seeQTL
rs6468807	NCALD	cis	cerebellum	SCAN
rs6468807	RRM2B	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102965400-102989800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr8:102976000-102992000	Weak transcription	Right Ventricle	heart
3	chr8:102981000-102992000	Weak transcription	Esophagus	oesophagus
4	chr8:102981400-102989800	Weak transcription	Aorta	Aorta
5	chr8:102983400-102991400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr8:102983600-102991200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr8:102983600-102992000	Weak transcription	Left Ventricle	heart
8	chr8:102985800-102989800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr8:102986400-102990400	Weak transcription	Fetal Heart	heart
10	chr8:102987200-102991000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr8:102987400-102988600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr8:102987400-102990800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr8:102987600-102988400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr8:102987800-102989800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr8:102987800-102992000	Weak transcription	Lung	lung
16	chr8:102988000-102988600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr8:102988000-102988800	ZNF genes & repeats	GM12878-XiMat	blood
18	chr8:102988000-102989800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr8:102988000-102989800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr8:102988000-102989800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr8:102988000-102989800	Weak transcription	NHEK	skin
22	chr8:102988200-102988600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr8:102988200-102988600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
24	chr8:102988200-102988600	ZNF genes & repeats	Ovary	ovary
25	chr8:102988200-102988600	ZNF genes & repeats	Spleen	Spleen
26	chr8:102988200-102991000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr8:102988200-102991200	Weak transcription	K562	blood

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