Variant report

Variant	rs7840045
Chromosome Location	chr8:102979756-102979757
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:102975291..102976986-chr8:102979593..102982495,2	MCF-7	breast:
2	chr8:102979732..102981930-chr8:102982441..102985992,3	K562	blood:
3	chr8:102974756..102976372-chr8:102978435..102981394,2	K562	blood:
4	chr8:102977498..102979940-chr8:102992806..102995177,2	K562	blood:
5	chr8:102962220..102965119-chr8:102979593..102981661,2	MCF-7	breast:
6	chr8:102974419..102976256-chr8:102977561..102979935,2	K562	blood:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10097554	0.92[CEU][hapmap]
rs10098273	0.89[EUR][1000 genomes]
rs10099842	1.00[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.95[TSI][hapmap];0.97[EUR][1000 genomes]
rs1119377	0.92[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs11778653	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12545403	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs13278642	0.85[CEU][hapmap]
rs1371739	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1371740	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1543771	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs17495818	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs1866690	0.85[EUR][1000 genomes]
rs1866691	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs1866692	0.86[EUR][1000 genomes]
rs1866693	0.85[EUR][1000 genomes]
rs2119226	0.89[CEU][hapmap]
rs4145554	0.96[CEU][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes]
rs4734042	0.82[CEU][hapmap]
rs4734043	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs4734044	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4734045	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4734046	0.86[EUR][1000 genomes]
rs4734047	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4734048	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs4734602	0.96[CEU][hapmap];0.96[EUR][1000 genomes]
rs4734603	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs4734604	0.97[EUR][1000 genomes]
rs4734606	0.92[CEU][hapmap];0.93[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs6468803	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6468804	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6468805	0.92[CEU][hapmap];0.86[GIH][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes]
rs6468806	0.86[EUR][1000 genomes]
rs6468807	0.92[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs6981347	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs6982001	0.96[CEU][hapmap];0.89[GIH][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes]
rs6991019	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6991178	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs6995105	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6999047	0.86[EUR][1000 genomes]
rs6999316	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7003320	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs7010848	0.94[ASW][hapmap];0.96[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7015981	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs718263	0.80[LWK][hapmap];0.90[YRI][hapmap]
rs7820244	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7823856	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs7838556	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs7838767	0.90[EUR][1000 genomes]
rs7839884	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7841927	0.86[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7840045	NCALD	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:102965400-102989800	Weak transcription	Stomach Smooth Muscle	stomach
2	chr8:102970400-102980800	Weak transcription	Psoas Muscle	Psoas
3	chr8:102970800-102979800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr8:102976000-102992000	Weak transcription	Right Ventricle	heart
5	chr8:102979000-102980400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr8:102979200-102980400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr8:102979400-102980200	Enhancers	NHDF-Ad	bronchial
8	chr8:102979400-102980400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr8:102979400-102980800	Enhancers	Fetal Heart	heart
10	chr8:102979400-102981400	Enhancers	Skeletal Muscle Male	skeletal muscle
11	chr8:102979400-102985600	Enhancers	Fetal Muscle Leg	muscle
12	chr8:102979600-102980000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr8:102979600-102980000	Enhancers	Aorta	Aorta
14	chr8:102979600-102980000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr8:102979600-102980200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr8:102979600-102980200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr8:102979600-102980200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr8:102979600-102980200	Enhancers	Fetal Muscle Trunk	muscle
19	chr8:102979600-102980200	Enhancers	Left Ventricle	heart
20	chr8:102979600-102980200	Enhancers	Rectal Smooth Muscle	rectum
21	chr8:102979600-102980200	Enhancers	Right Atrium	heart
22	chr8:102979600-102980400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr8:102979600-102981000	Enhancers	Ovary	ovary

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