Variant report

Variant	rs946779
Chromosome Location	chr10:99494740-99494741
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:99460267..99463088-chr10:99494596..99496762,2	K562	blood:
2	chr10:99445750..99450066-chr10:99494053..99497713,5	MCF-7	breast:
3	chr10:99472472..99476089-chr10:99494153..99498366,9	MCF-7	breast:
4	chr10:99493636..99495649-chr10:99496310..99499627,3	K562	blood:

Variant related genes	Relation type
ENSG00000155254	Chromatin interaction
ENSG00000119986	Chromatin interaction
ENSG00000155256	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10748707	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10786368	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10786369	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12415272	0.82[YRI][hapmap]
rs1253023	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3818876	1.00[ASW][hapmap];0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.95[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3829137	0.84[MEX][hapmap]
rs4593946	0.84[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.92[MEX][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4917783	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4917784	0.82[ASW][hapmap];0.88[CEU][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4917785	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4919135	0.95[YRI][hapmap]
rs7076831	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7900119	0.95[YRI][hapmap]
rs7915100	0.95[YRI][hapmap]
rs946780	0.84[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.92[ASN][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	esv1817777	chr10:99196035-99558169	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv467441	chr10:99472710-99541104	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
3	nsv552026	chr10:99472710-99541104	Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs946779	FBXW4	cis	parietal	SCAN
rs946779	PI4K2A	cis	parietal	SCAN
rs946779	MARVELD1	cis	lung	GTEx
rs946779	SEMA4G	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:99478800-99496400	Weak transcription	Primary hematopoietic stem cells	blood
2	chr10:99486800-99496000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr10:99486800-99496200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr10:99486800-99496400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr10:99486800-99496400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr10:99486800-99496400	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr10:99486800-99496400	Weak transcription	Pancreas	Pancrea
8	chr10:99486800-99496600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr10:99487000-99496000	Weak transcription	K562	blood
10	chr10:99487000-99496400	Weak transcription	Brain Anterior Caudate	brain
11	chr10:99487000-99496400	Weak transcription	Colon Smooth Muscle	Colon
12	chr10:99487000-99496400	Weak transcription	A549	lung
13	chr10:99487200-99496400	Weak transcription	NHEK	skin
14	chr10:99487200-99496600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr10:99487600-99496000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr10:99489200-99496200	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr10:99491600-99496400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr10:99491600-99496400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr10:99491600-99496400	Weak transcription	Brain Substantia Nigra	brain
20	chr10:99491600-99496400	Weak transcription	NHDF-Ad	bronchial
21	chr10:99491600-99496400	Weak transcription	NHLF	lung
22	chr10:99491800-99495400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr10:99491800-99496200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr10:99491800-99496400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr10:99492000-99496000	Weak transcription	Hela-S3	cervix
26	chr10:99492000-99496000	Weak transcription	HMEC	breast
27	chr10:99492000-99496400	Weak transcription	HSMM	muscle
28	chr10:99492000-99496400	Weak transcription	Osteobl	bone
29	chr10:99492200-99496400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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