Variant report

Variant	rs1119377
Chromosome Location	chr8:102986802-102986803
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10097554	0.84[CEU][hapmap]
rs10098273	0.90[EUR][1000 genomes]
rs10099842	0.92[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs10105502	0.89[YRI][hapmap]
rs11778653	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs11786660	0.80[JPT][hapmap]
rs12545403	0.96[CEU][hapmap];0.89[CHB][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];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17495818	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs1866690	0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1866691	0.96[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1866692	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1866693	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2023269	0.89[YRI][hapmap]
rs2119226	0.89[CEU][hapmap]
rs4145554	0.96[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs4734042	0.82[CEU][hapmap];0.84[CHB][hapmap]
rs4734043	1.00[CEU][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4734044	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4734045	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4734046	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4734047	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4734048	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[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];0.87[CHD][hapmap];0.95[GIH][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][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];0.85[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6468806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6468807	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]
rs6981347	1.00[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6982001	0.94[ASW][hapmap];0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6991019	0.96[CEU][hapmap];0.85[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];0.93[GIH][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs6999047	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6999316	1.00[CEU][hapmap];0.85[CHB][hapmap];0.90[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7003320	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7010848	0.96[CEU][hapmap];0.93[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];0.93[GIH][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs7823856	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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];0.89[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs7841927	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1119377	RRM2B	cis	parietal	SCAN
rs1119377	NCALD	cis	cerebellum	SCAN
rs1119377	STK3	cis	cerebellum	SCAN

Chromatin state (count:24 , 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	chr8:102980000-102987200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr8:102980200-102988200	Weak transcription	Spleen	Spleen
5	chr8:102981000-102987400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr8:102981000-102992000	Weak transcription	Esophagus	oesophagus
7	chr8:102981400-102989800	Weak transcription	Aorta	Aorta
8	chr8:102983400-102991400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr8:102983600-102991200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr8:102983600-102992000	Weak transcription	Left Ventricle	heart
11	chr8:102985600-102987800	Weak transcription	Fetal Muscle Leg	muscle
12	chr8:102985800-102987600	Enhancers	Psoas Muscle	Psoas
13	chr8:102985800-102989800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr8:102986000-102988000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr8:102986200-102988000	Enhancers	NHEK	skin
16	chr8:102986400-102988000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr8:102986400-102990400	Weak transcription	Fetal Heart	heart
18	chr8:102986600-102987000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr8:102986600-102987000	Active TSS	GM12878-XiMat	blood
20	chr8:102986600-102987200	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr8:102986600-102987400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr8:102986600-102987800	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr8:102986800-102987000	Enhancers	Ovary	ovary
24	chr8:102986800-102987200	Enhancers	Fetal Lung	lung

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