Variant report

Variant	rs10099842
Chromosome Location	chr8:102974357-102974358
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:102970883..102973070-chr8:102973117..102975450,3	MCF-7	breast:
2	chr8:102968258..102970175-chr8:102971587..102974473,2	MCF-7	breast:
3	chr8:102970055..102972345-chr8:102973060..102976868,3	MCF-7	breast:

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10097554	0.92[CEU][hapmap]
rs10098273	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10955277	0.83[ASN][1000 genomes]
rs1119377	0.92[CEU][hapmap];0.93[GIH][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap];0.88[EUR][1000 genomes]
rs11778653	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs12545403	0.96[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13278642	0.85[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs1371739	1.00[EUR][1000 genomes]
rs1371740	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1543771	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs17495818	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1866690	0.87[EUR][1000 genomes]
rs1866691	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs1866692	0.87[EUR][1000 genomes]
rs1866693	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2119226	0.89[CEU][hapmap]
rs4145554	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]
rs4734042	0.82[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes]
rs4734043	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4734044	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4734045	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4734046	0.88[EUR][1000 genomes]
rs4734047	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4734048	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs4734602	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4734603	1.00[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4734604	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4734606	0.92[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.85[JPT][hapmap];0.96[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6468803	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs6468804	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs6468805	0.92[CEU][hapmap];0.83[CHD][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs6468806	0.88[EUR][1000 genomes]
rs6468807	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]
rs6981347	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs6982001	0.96[CEU][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6991019	0.96[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs6991178	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6995105	1.00[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.98[EUR][1000 genomes]
rs6999047	0.88[EUR][1000 genomes]
rs6999316	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs7003320	0.92[CEU][hapmap];0.85[JPT][hapmap]
rs7010848	0.96[CEU][hapmap];1.00[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs7015981	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7820244	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7823856	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs7838556	0.96[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7838767	0.86[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7839884	1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7840045	1.00[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs7841927	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv972563	chr8:102970051-102975959	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
5	esv2761453	chr8:102970136-102974682	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10099842	LRP12	cis	cerebellum	SCAN
rs10099842	MATN2	cis	cerebellum	SCAN
rs10099842	NCALD	cis	cerebellum	SCAN

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102965400-102989800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr8:102969200-102979600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr8:102970000-102974400	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr8:102970400-102979600	Weak transcription	Left Ventricle	heart
5	chr8:102970400-102980800	Weak transcription	Psoas Muscle	Psoas
6	chr8:102970800-102979800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr8:102971800-102979200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr8:102972200-102975800	Enhancers	GM12878-XiMat	blood
9	chr8:102972600-102979400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr8:102973600-102974800	Enhancers	Colon Smooth Muscle	Colon
11	chr8:102973600-102975000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr8:102973600-102975000	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr8:102973800-102974800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr8:102973800-102974800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr8:102973800-102974800	Enhancers	Aorta	Aorta
16	chr8:102973800-102974800	Enhancers	Fetal Muscle Leg	muscle
17	chr8:102973800-102974800	Enhancers	Ovary	ovary
18	chr8:102973800-102974800	Enhancers	Rectal Smooth Muscle	rectum
19	chr8:102973800-102974800	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr8:102973800-102975000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr8:102974200-102974800	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr8:102974200-102975000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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