Variant report

Variant	rs10008894
Chromosome Location	chr4:86763097-86763098
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	chr4:86762784..86764294-chr4:86767286..86769112,2	MCF-7	breast:

Extended variants
information (count: 13 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10002566	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10031413	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1510584	1.00[CEU][hapmap];0.87[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3796625	0.87[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs61138111	0.95[ASN][1000 genomes]
rs72980807	0.87[ASN][1000 genomes]
rs73833889	0.96[ASN][1000 genomes]
rs882639	0.82[EUR][1000 genomes]
rs896656	0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3450999	chr4:86485840-86773745	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases
2	nsv879518	chr4:86739805-86778943	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv830000	chr4:86745341-86909059	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv470049	chr4:86750699-86776488	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10008894	C4orf11	cis	parietal	SCAN
rs10008894	FAM13A	cis	cerebellum	SCAN
rs10008894	LIN54	cis	cerebellum	SCAN
rs10008894	PIGY	cis	cerebellum	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86737600-86763200	Weak transcription	Primary B cells from cord blood	blood
2	chr4:86749400-86787600	Weak transcription	Pancreas	Pancrea
3	chr4:86749600-86763600	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr4:86750000-86809200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr4:86758000-86763600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:86758600-86763800	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr4:86759000-86763400	Weak transcription	NHLF	lung
8	chr4:86759000-86763400	Weak transcription	Osteobl	bone
9	chr4:86759400-86763400	Weak transcription	Adipose Nuclei	Adipose
10	chr4:86759400-86763800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr4:86760000-86782600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:86760200-86763200	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr4:86760200-86763400	Weak transcription	Fetal Kidney	kidney
14	chr4:86761200-86763200	Enhancers	HUVEC	blood vessel
15	chr4:86761600-86763200	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr4:86761800-86763200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:86761800-86763200	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:86761800-86763200	Weak transcription	Stomach Mucosa	stomach
19	chr4:86761800-86763200	Weak transcription	Stomach Smooth Muscle	stomach
20	chr4:86761800-86763400	Weak transcription	HSMM	muscle
21	chr4:86761800-86763400	Weak transcription	HSMMtube	muscle
22	chr4:86761800-86763800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:86761800-86763800	Weak transcription	Left Ventricle	heart
24	chr4:86761800-86778800	Weak transcription	Fetal Lung	lung
25	chr4:86762000-86763200	Weak transcription	Rectal Smooth Muscle	rectum
26	chr4:86762000-86763800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:86762200-86763400	Weak transcription	NHDF-Ad	bronchial
28	chr4:86762200-86769200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:86762400-86764200	Enhancers	Primary B cells from peripheral blood	blood
30	chr4:86762400-86764200	Enhancers	Fetal Brain Male	brain
31	chr4:86762800-86764200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr4:86763000-86763400	Enhancers	Brain Germinal Matrix	brain
33	chr4:86763000-86764000	Enhancers	Primary hematopoietic stem cells	blood
34	chr4:86763000-86764000	Enhancers	Colon Smooth Muscle	Colon

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