Variant report

Variant	rs4145554
Chromosome Location	chr8:102966148-102966149
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	chr8:102958971..102963759-chr8:102964426..102969369,7	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10097554	0.88[CEU][hapmap]
rs10098273	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10099842	0.88[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10955277	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1119377	0.96[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs11778653	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12545403	1.00[CEU][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13278642	0.81[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1371739	0.93[EUR][1000 genomes]
rs1371740	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs1543771	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs17495818	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1866690	0.91[EUR][1000 genomes]
rs1866691	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs1866692	0.91[EUR][1000 genomes]
rs1866693	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1992330	0.81[YRI][hapmap]
rs2119226	0.92[CEU][hapmap]
rs4734042	0.85[CEU][hapmap];0.83[AMR][1000 genomes]
rs4734043	0.96[CEU][hapmap];0.91[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4734044	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4734045	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4734046	0.92[EUR][1000 genomes]
rs4734047	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4734048	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs4734602	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4734603	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4734604	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4734606	0.96[CEU][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6468803	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6468804	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs6468805	0.96[CEU][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes]
rs6468806	0.92[EUR][1000 genomes]
rs6468807	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]
rs6981347	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs6982001	0.92[CEU][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes]
rs6991019	1.00[CEU][hapmap];0.91[GIH][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs6991178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6995105	0.96[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs6999047	0.92[EUR][1000 genomes]
rs6999316	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7003320	0.96[CEU][hapmap];0.85[JPT][hapmap];0.83[EUR][1000 genomes]
rs7010848	1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes]
rs7015981	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7820244	0.96[CEU][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs7823856	0.96[CEU][hapmap];0.92[EUR][1000 genomes]
rs7838556	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7838767	0.91[CHB][hapmap];0.85[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7839884	0.96[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7840045	0.96[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs7841927	0.92[EUR][1000 genomes]

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
rs4145554	STK3	cis	cerebellum	SCAN
rs4145554	NCALD	cis	cerebellum	SCAN
rs4145554	MATN2	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102957600-102970200	Weak transcription	Esophagus	oesophagus
2	chr8:102960800-102966400	Weak transcription	Primary T cells from cord blood	blood
3	chr8:102961000-102971200	Weak transcription	Aorta	Aorta
4	chr8:102962800-102966200	Weak transcription	Primary T cells fromperipheralblood	blood
5	chr8:102963000-102968000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr8:102963000-102969600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr8:102963000-102969800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr8:102963200-102968200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr8:102963200-102969800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr8:102963200-102973600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr8:102964400-102966400	Enhancers	Fetal Muscle Trunk	muscle
12	chr8:102964400-102966600	Enhancers	Left Ventricle	heart
13	chr8:102964400-102966800	Enhancers	Right Ventricle	heart
14	chr8:102964600-102966400	Enhancers	Psoas Muscle	Psoas
15	chr8:102964600-102967000	Enhancers	Skeletal Muscle Female	skeletal muscle
16	chr8:102965000-102966200	Enhancers	Fetal Brain Female	brain
17	chr8:102965200-102970800	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr8:102965400-102966200	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr8:102965400-102969600	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr8:102965400-102969800	Weak transcription	NHDF-Ad	bronchial
21	chr8:102965400-102971000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr8:102965400-102989800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr8:102965600-102968600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr8:102965600-102969600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr8:102965600-102969600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr8:102965600-102969800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr8:102965600-102969800	Weak transcription	Ovary	ovary
28	chr8:102965800-102968600	Weak transcription	Fetal Brain Male	brain
29	chr8:102965800-102969600	Weak transcription	Fetal Muscle Leg	muscle
30	chr8:102966000-102966600	Weak transcription	GM12878-XiMat	blood
31	chr8:102966000-102966800	Enhancers	Fetal Heart	heart
32	chr8:102966000-102969800	Weak transcription	Right Atrium	heart

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