Variant report

Variant	rs462587
Chromosome Location	chr5:75944276-75944277
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	chr5:75934487..75936821-chr5:75943605..75946585,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1423605	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431361	0.83[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2431362	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431363	0.88[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];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431364	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2431366	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432187	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2432188	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432189	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2455213	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455215	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455229	0.85[CHB][hapmap];0.89[JPT][hapmap]
rs2455234	0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs32947	0.81[CHB][hapmap];0.80[GIH][hapmap]
rs399058	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs429703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430389	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs457054	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs457182	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs457205	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs458573	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs458581	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs458661	0.97[ASN][1000 genomes]
rs460294	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs460374	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs460431	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs460482	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs460562	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs461187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs461273	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];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs461475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs463147	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs463973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs465988	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs615951	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.99[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	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
2	nsv1031881	chr5:75917033-75946265	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv1017025	chr5:75926278-75946265	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv1035135	chr5:75927027-76092058	Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs462587	FAM169A	cis	parietal	SCAN

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75882600-75969400	Weak transcription	Stomach Mucosa	stomach
2	chr5:75914200-75953800	Weak transcription	Colonic Mucosa	Colon
3	chr5:75919200-75955400	Weak transcription	Fetal Kidney	kidney
4	chr5:75923000-75944400	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr5:75929800-75945400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr5:75930400-75944400	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr5:75932200-75945400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr5:75934400-75945000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr5:75934800-75944600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:75935000-75945000	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:75935000-75945400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr5:75935200-75945000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr5:75938800-75945400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:75943000-75945600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
15	chr5:75943200-75944400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr5:75943200-75946000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
17	chr5:75943400-75944800	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr5:75943400-75946000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr5:75943400-75946000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr5:75943400-75946200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:75943400-75946200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
22	chr5:75943600-75944400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
23	chr5:75943600-75944400	ZNF genes & repeats	Fetal Intestine Large	intestine
24	chr5:75943600-75944400	ZNF genes & repeats	GM12878-XiMat	blood
25	chr5:75943600-75944600	Strong transcription	HepG2	liver
26	chr5:75943600-75944800	Enhancers	Osteobl	bone
27	chr5:75943600-75945000	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
28	chr5:75943600-75945200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
29	chr5:75943600-75945600	ZNF genes & repeats	Liver	Liver
30	chr5:75943600-75946000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
31	chr5:75943600-75946000	ZNF genes & repeats	Primary B cells from cord blood	blood
32	chr5:75943600-75946000	ZNF genes & repeats	Placenta	Placenta
33	chr5:75943600-75946000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
34	chr5:75943600-75946200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
35	chr5:75943600-75946200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
36	chr5:75943600-75947000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr5:75943800-75944400	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
38	chr5:75943800-75945000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
39	chr5:75943800-75945200	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
40	chr5:75943800-75945200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
41	chr5:75943800-75946000	ZNF genes & repeats	Primary T cells from cord blood	blood
42	chr5:75943800-75946000	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
43	chr5:75943800-75946200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr5:75943800-75986600	Weak transcription	Gastric	stomach
45	chr5:75944000-75945400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr5:75944000-75945400	Weak transcription	Spleen	Spleen
47	chr5:75944000-75946000	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
48	chr5:75944000-75946000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
49	chr5:75944000-75946200	Strong transcription	Rectal Mucosa Donor 31	rectum
50	chr5:75944200-75944400	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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