Variant report

Variant	rs461273
Chromosome Location	chr5:75946138-75946139
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr5:75944771-75946139	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75934487..75936821-chr5:75943605..75946585,2	MCF-7	breast:

Variant related genes	Relation type
IQGAP2	TF binding region

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

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

rs_ID	r²[population]
rs1423605	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2252231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431361	0.83[ASW][hapmap];1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2431362	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[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];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2431364	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2431366	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432187	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2432188	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2432189	0.88[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[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];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455215	0.99[AMR][1000 genomes];0.98[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	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs429703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs430389	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456572	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs456708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs457054	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs457182	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs457205	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs458573	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs458581	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[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];0.81[YRI][hapmap]
rs460374	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs460431	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs460482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[AMR][1000 genomes];0.99[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];0.92[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs461475	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs462587	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]
rs463147	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs463973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs465988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs466393	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[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];0.84[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
rs461273	FAM169A	cis	parietal	SCAN

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

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	chr5:75943400-75946200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr5:75943400-75946200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
6	chr5:75943600-75946200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
7	chr5:75943600-75946200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
8	chr5:75943600-75947000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr5:75943800-75946200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr5:75943800-75986600	Weak transcription	Gastric	stomach
11	chr5:75944000-75946200	Strong transcription	Rectal Mucosa Donor 31	rectum
12	chr5:75944400-75946200	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
13	chr5:75944400-75949800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr5:75944800-75948400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:75945000-75946200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
16	chr5:75945000-75946200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr5:75945000-75949600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr5:75945000-75950600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr5:75945200-75948000	Weak transcription	HepG2	liver
20	chr5:75945200-75951000	Strong transcription	Primary T helper cells PMA-I stimulated	--
21	chr5:75945200-75976200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr5:75945200-75976400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr5:75945200-76001000	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr5:75945600-75948000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr5:75945600-75976600	Strong transcription	Liver	Liver
26	chr5:75945800-75970400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:75946000-75946400	Weak transcription	Primary monocytes fromperipheralblood	blood
28	chr5:75946000-75946400	Strong transcription	Placenta	Placenta
29	chr5:75946000-75946600	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr5:75946000-75946800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr5:75946000-75947000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr5:75946000-75947800	Weak transcription	Primary T cells from cord blood	blood
33	chr5:75946000-75948000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr5:75946000-75948000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr5:75946000-75948200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr5:75946000-75948400	Weak transcription	Primary neutrophils fromperipheralblood	blood
37	chr5:75946000-75948400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr5:75946000-75948400	Weak transcription	Fetal Intestine Small	intestine
39	chr5:75946000-75948600	Weak transcription	Primary B cells from cord blood	blood
40	chr5:75946000-75951000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr5:75946000-75953000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr5:75946000-75953000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:75946000-75953000	Weak transcription	Duodenum Mucosa	Duodenum
44	chr5:75946000-75953000	Weak transcription	Spleen	Spleen
45	chr5:75946000-75953800	Weak transcription	Pancreas	Pancrea
46	chr5:75946000-75953800	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr5:75946000-75955200	Weak transcription	Aorta	Aorta
48	chr5:75946000-75958600	Weak transcription	Fetal Stomach	stomach
49	chr5:75946000-75959000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr5:75946000-75967000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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