Variant report

Variant	rs42407
Chromosome Location	chr5:14361471-14361472
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:14360819..14363309-chr5:14376690..14379574,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs154152	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs154159	0.96[ASN][1000 genomes]
rs154161	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1664507	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs247134	0.92[EUR][1000 genomes]
rs247139	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs247140	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs247142	0.95[CEU][hapmap];0.85[JPT][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs247143	0.90[EUR][1000 genomes]
rs247144	0.92[EUR][1000 genomes]
rs256416	0.86[ASN][1000 genomes]
rs256417	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs256423	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs30623	0.85[JPT][hapmap]
rs30624	0.85[JPT][hapmap]
rs30769	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs30770	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs30771	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs30782	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs30783	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30784	1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs30792	0.82[ASW][hapmap];0.90[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.93[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs39857	0.95[CEU][hapmap];0.85[EUR][1000 genomes]
rs39866	1.00[ASN][1000 genomes]
rs409214	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs415341	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs42259	0.95[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs42551	0.95[CEU][hapmap];0.89[TSI][hapmap];0.85[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	nsv948355	chr5:14160447-14395478	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv1026914	chr5:14237782-14751588	Weak transcription Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv830210	chr5:14255039-14431552	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs42407	FAM105B	cis	cerebellum	SCAN
rs42407	LOC285696	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:14342800-14365200	Weak transcription	Small Intestine	intestine
2	chr5:14343800-14362400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr5:14350400-14373800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:14351600-14399400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr5:14353600-14366200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:14353600-14385200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:14353600-14398800	Strong transcription	Rectal Mucosa Donor 29	rectum
8	chr5:14354400-14374800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr5:14354600-14402400	Strong transcription	Liver	Liver
10	chr5:14355000-14392400	Strong transcription	HSMMtube	muscle
11	chr5:14355000-14398800	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr5:14355400-14365200	Strong transcription	HSMM	muscle
13	chr5:14355600-14375000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:14356000-14362400	Strong transcription	Osteobl	bone
15	chr5:14356000-14366200	Strong transcription	Muscle Satellite Cultured Cells	--
16	chr5:14356400-14365400	Strong transcription	NHEK	skin
17	chr5:14356400-14373800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr5:14356600-14363800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:14356600-14365200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr5:14356800-14370200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:14356800-14376000	Strong transcription	HepG2	liver
22	chr5:14357000-14370400	Strong transcription	Fetal Intestine Small	intestine
23	chr5:14357000-14371200	Strong transcription	Sigmoid Colon	Sigmoid Colon
24	chr5:14357000-14374000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr5:14357000-14376400	Strong transcription	NHLF	lung
26	chr5:14357000-14376600	Strong transcription	Duodenum Mucosa	Duodenum
27	chr5:14357200-14362200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:14357400-14361600	Strong transcription	Placenta	Placenta
29	chr5:14357600-14361600	Strong transcription	Aorta	Aorta
30	chr5:14357600-14361800	Strong transcription	Ovary	ovary
31	chr5:14357600-14362400	Strong transcription	Gastric	stomach
32	chr5:14357600-14363000	Strong transcription	A549	lung
33	chr5:14357600-14365200	Strong transcription	Primary B cells from peripheral blood	blood
34	chr5:14357600-14422000	Weak transcription	Stomach Mucosa	stomach
35	chr5:14357800-14385000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr5:14357800-14389800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr5:14358000-14361600	Strong transcription	Thymus	Thymus
38	chr5:14358000-14373800	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr5:14358000-14377000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr5:14358000-14385800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr5:14358000-14389800	Strong transcription	Adipose Nuclei	Adipose
42	chr5:14358200-14362000	Strong transcription	Pancreas	Pancrea
43	chr5:14358200-14362400	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr5:14358200-14362800	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr5:14358200-14366000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr5:14358200-14366000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr5:14358200-14375800	Strong transcription	Stomach Smooth Muscle	stomach
48	chr5:14358200-14391600	Strong transcription	Primary B cells from cord blood	blood
49	chr5:14358400-14361600	Strong transcription	Hela-S3	cervix
50	chr5:14358400-14362000	Strong transcription	Fetal Thymus	thymus

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