Variant report

Variant	rs2451855
Chromosome Location	chr5:16584227-16584228
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:16577162..16580474-chr5:16583638..16586521,3	MCF-7	breast:
2	chr5:16577676..16580941-chr5:16582189..16586155,5	K562	blood:
3	chr5:16577676..16580941-chr5:16584093..16586155,5	K562	blood:

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

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

rs_ID	r²[population]
rs173963	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs173972	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17541267	0.93[CEU][hapmap]
rs17650584	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17650599	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17650706	0.91[ASN][1000 genomes]
rs17707133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2447809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2447810	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];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2447811	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2447812	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]
rs2447813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2447815	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2447816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447817	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2447818	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2451848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2451849	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]
rs2451850	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]
rs2451852	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];0.80[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2451853	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2451854	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2451856	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs256878	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2592038	0.93[CEU][hapmap]
rs2617419	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2927607	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs398274	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs403565	0.93[CEU][hapmap];0.82[MEX][hapmap]
rs431154	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs448021	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs604535	0.97[ASN][1000 genomes]
rs62369751	1.00[ASN][1000 genomes]
rs62371269	0.97[ASN][1000 genomes]
rs62371271	0.88[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
rs2451855	MARCH11	cis	cerebellum	SCAN
rs2451855	FAM134B	cis	cerebellum	SCAN

Chromatin state (count:41 , 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	chr5:16543600-16589800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr5:16571400-16587200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr5:16571400-16588200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr5:16573800-16585200	Weak transcription	Pancreas	Pancrea
6	chr5:16574200-16585200	Weak transcription	Fetal Intestine Small	intestine
7	chr5:16574800-16589800	Weak transcription	Thymus	Thymus
8	chr5:16575000-16588000	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr5:16575200-16585800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr5:16575600-16591600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:16575800-16587600	Weak transcription	Primary T helper cells fromperipheralblood	blood
12	chr5:16576000-16587200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr5:16578400-16606800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr5:16579200-16586800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr5:16579400-16593200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr5:16579600-16585400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:16581000-16585200	Weak transcription	Liver	Liver
18	chr5:16581000-16598400	Weak transcription	Stomach Smooth Muscle	stomach
19	chr5:16581200-16588600	Weak transcription	Fetal Heart	heart
20	chr5:16581400-16585400	Weak transcription	Brain Anterior Caudate	brain
21	chr5:16581400-16587000	Weak transcription	Primary T cells from cord blood	blood
22	chr5:16581400-16593200	Weak transcription	Right Ventricle	heart
23	chr5:16581400-16596000	Weak transcription	Fetal Brain Female	brain
24	chr5:16581600-16585200	Weak transcription	Left Ventricle	heart
25	chr5:16581600-16585600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr5:16581600-16585800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:16581800-16585400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr5:16581800-16585400	Weak transcription	Brain Angular Gyrus	brain
29	chr5:16582400-16585200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr5:16583200-16585200	Weak transcription	Right Atrium	heart
31	chr5:16583200-16585600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr5:16583200-16586000	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr5:16583400-16591400	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr5:16583400-16599600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr5:16583800-16585800	Enhancers	Brain Substantia Nigra	brain
36	chr5:16584000-16584400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr5:16584000-16584400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr5:16584000-16585800	Weak transcription	GM12878-XiMat	blood
39	chr5:16584200-16585200	Weak transcription	Brain Hippocampus Middle	brain
40	chr5:16584200-16585200	Weak transcription	Gastric	stomach
41	chr5:16584200-16586000	Weak transcription	Brain Cingulate Gyrus	brain

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