Variant report

Variant	rs10000250
Chromosome Location	chr4:15482477-15482478
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:15479740..15482605-chr4:15655501..15658427,3	MCF-7	breast:
2	chr4:15481667..15484454-chr4:15772642..15775403,2	MCF-7	breast:
3	chr4:15480883..15483744-chr4:15651050..15653259,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118564	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10012928	1.00[ASN][1000 genomes]
rs10022530	0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10212846	1.00[ASN][1000 genomes]
rs1024757	0.83[ASN][1000 genomes]
rs1024760	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4423869	0.93[CEU][hapmap]
rs4698110	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4698382	0.88[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838330	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs719993	0.80[CEU][hapmap]
rs9990934	0.80[CEU][hapmap]
rs9993580	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993656	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9994702	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9995927	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10000250	FAM200B	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15481200-15485200	Weak transcription	Right Ventricle	heart
2	chr4:15481400-15486200	Weak transcription	Spleen	Spleen
3	chr4:15481600-15482600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr4:15481600-15482600	Enhancers	Adipose Nuclei	Adipose
5	chr4:15481600-15482600	Enhancers	Fetal Heart	heart
6	chr4:15481600-15484000	Weak transcription	Aorta	Aorta
7	chr4:15481600-15484200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:15481600-15484400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr4:15481600-15484400	Weak transcription	Placenta	Placenta
10	chr4:15481600-15484400	Weak transcription	K562	blood
11	chr4:15481600-15484600	Weak transcription	Right Atrium	heart
12	chr4:15481600-15488000	Weak transcription	HSMMtube	muscle
13	chr4:15481600-15490200	Weak transcription	Esophagus	oesophagus
14	chr4:15481600-15498600	Weak transcription	Liver	Liver
15	chr4:15481600-15519000	Weak transcription	Gastric	stomach
16	chr4:15481800-15482600	Enhancers	Brain Angular Gyrus	brain
17	chr4:15481800-15482600	Enhancers	Colon Smooth Muscle	Colon
18	chr4:15481800-15483200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr4:15481800-15483200	Weak transcription	Fetal Kidney	kidney
20	chr4:15481800-15484000	Weak transcription	Ovary	ovary
21	chr4:15481800-15488200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr4:15482000-15482600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr4:15482000-15482600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:15482000-15482600	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr4:15482000-15482600	Enhancers	Brain Germinal Matrix	brain
26	chr4:15482000-15482600	Genic enhancers	Stomach Smooth Muscle	stomach
27	chr4:15482000-15482600	Enhancers	HMEC	breast
28	chr4:15482000-15482600	Genic enhancers	Osteobl	bone
29	chr4:15482000-15482800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:15482000-15482800	Enhancers	NH-A	brain
31	chr4:15482000-15483200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr4:15482000-15484000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr4:15482000-15484200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr4:15482000-15485400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr4:15482000-15486400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr4:15482000-15486600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr4:15482000-15487000	Weak transcription	HSMM	muscle
38	chr4:15482000-15487600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr4:15482000-15489600	Weak transcription	Brain Substantia Nigra	brain
40	chr4:15482000-15491000	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr4:15482000-15491800	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr4:15482200-15482600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr4:15482200-15482600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:15482200-15482600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:15482200-15482600	Genic enhancers	Fetal Muscle Trunk	muscle
46	chr4:15482200-15482600	Flanking Active TSS	Hela-S3	cervix
47	chr4:15482200-15482800	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
48	chr4:15482200-15484000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr4:15482200-15484600	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr4:15482200-15484600	Weak transcription	NHEK	skin

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