Variant report

Variant	rs2451850
Chromosome Location	chr5:16589991-16589992
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	chr5:16588327..16590123-chr5:16591920..16594377,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs173963	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs173972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17541267	0.93[CEU][hapmap]
rs17650584	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17650599	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs17650706	0.94[ASN][1000 genomes]
rs17707133	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2447809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2447810	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];0.87[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2447811	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2447812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447815	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2447817	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2447818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2451848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2451849	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451852	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451854	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451855	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2451856	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2560825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs256878	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2592038	0.93[CEU][hapmap]
rs2617419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2927607	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs398274	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403565	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs431154	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs448021	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs604535	1.00[ASN][1000 genomes]
rs62369751	0.97[ASN][1000 genomes]
rs62371269	1.00[ASN][1000 genomes]
rs62371271	0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881187	chr5:16514269-16654960	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2451850	FAM134B	cis	cerebellum	SCAN
rs2451850	MARCH11	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:16543200-16591600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr5:16575600-16591600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:16578400-16606800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:16579400-16593200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:16581000-16598400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr5:16581400-16593200	Weak transcription	Right Ventricle	heart
7	chr5:16581400-16596000	Weak transcription	Fetal Brain Female	brain
8	chr5:16583400-16591400	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr5:16583400-16599600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:16584400-16591200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:16584400-16592400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr5:16585400-16615600	Weak transcription	Primary B cells from cord blood	blood
13	chr5:16585600-16600000	Weak transcription	Gastric	stomach
14	chr5:16585800-16605000	Weak transcription	Fetal Intestine Large	intestine
15	chr5:16586000-16594800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr5:16586600-16593200	Weak transcription	Brain Germinal Matrix	brain
17	chr5:16587000-16591000	Strong transcription	Primary T cells from cord blood	blood
18	chr5:16587200-16590200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr5:16587200-16590400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr5:16587400-16591600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr5:16587400-16593200	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr5:16587400-16600400	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr5:16587600-16590400	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr5:16587600-16596400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr5:16587600-16598200	Weak transcription	Fetal Intestine Small	intestine
26	chr5:16587800-16590600	Enhancers	Brain Substantia Nigra	brain
27	chr5:16588000-16590600	Enhancers	Liver	Liver
28	chr5:16588200-16590400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr5:16588400-16590200	Enhancers	Pancreas	Pancrea
30	chr5:16588400-16590400	Enhancers	HepG2	liver
31	chr5:16588600-16590000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
32	chr5:16588600-16590000	Enhancers	Right Atrium	heart
33	chr5:16588600-16593200	Weak transcription	Left Ventricle	heart
34	chr5:16588800-16595400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:16589000-16593000	Weak transcription	Brain Angular Gyrus	brain
36	chr5:16589000-16593400	Weak transcription	Stomach Mucosa	stomach
37	chr5:16589000-16614800	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr5:16589200-16591600	Weak transcription	Brain Anterior Caudate	brain
39	chr5:16589400-16590800	Weak transcription	Fetal Heart	heart
40	chr5:16589400-16591000	Weak transcription	Adipose Nuclei	Adipose
41	chr5:16589400-16591400	Weak transcription	Brain Hippocampus Middle	brain
42	chr5:16589600-16590000	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr5:16589600-16590800	Weak transcription	Brain Cingulate Gyrus	brain
44	chr5:16589800-16590400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr5:16589800-16591000	Strong transcription	Thymus	Thymus

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