Variant report

Variant	rs2431361
Chromosome Location	chr5:75949043-75949044
allele	G/T
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	RUNX3	chr5:75948649-75949069	GM12878	blood:	n/a	n/a
2	NFYB	chr5:75948800-75949052	GM12878	blood:	n/a	n/a
3	TBL1XR1	chr5:75948957-75949073	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:75946272..75949133-chr5:75949218..75950979,2	MCF-7	breast:

Variant related genes	Relation type
IQGAP2	TF binding region
ENSG00000145703	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1423605	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2252231	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2431362	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2431363	1.00[CEU][hapmap];0.98[GIH][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2431364	0.84[EUR][1000 genomes]
rs2431366	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2432186	1.00[CEU][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2432187	0.91[EUR][1000 genomes]
rs2432188	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2432189	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2455213	1.00[CEU][hapmap];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2455215	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs399058	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs429703	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs430389	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs456572	1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs456708	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs457054	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs457182	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs457205	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs458573	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs458581	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs458661	0.80[ASN][1000 genomes]
rs460294	0.96[CEU][hapmap];1.00[YRI][hapmap]
rs460374	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs460431	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs460482	1.00[CEU][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]
rs461187	1.00[CEU][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs461273	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]
rs461475	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs462587	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]
rs463147	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs463973	1.00[CEU][hapmap];0.86[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs465988	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs466393	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs615951	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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
rs2431361	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	chr5:75943800-75986600	Weak transcription	Gastric	stomach
5	chr5:75944400-75949800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr5:75945000-75949600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr5:75945000-75950600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr5:75945200-75951000	Strong transcription	Primary T helper cells PMA-I stimulated	--
9	chr5:75945200-75976200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr5:75945200-75976400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:75945200-76001000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr5:75945600-75976600	Strong transcription	Liver	Liver
13	chr5:75945800-75970400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr5:75946000-75951000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:75946000-75953000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:75946000-75953000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:75946000-75953000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr5:75946000-75953000	Weak transcription	Spleen	Spleen
19	chr5:75946000-75953800	Weak transcription	Pancreas	Pancrea
20	chr5:75946000-75953800	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr5:75946000-75955200	Weak transcription	Aorta	Aorta
22	chr5:75946000-75958600	Weak transcription	Fetal Stomach	stomach
23	chr5:75946000-75959000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr5:75946000-75967000	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr5:75946200-75950400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:75946200-75953600	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr5:75946200-75953800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr5:75946200-75954000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr5:75946200-75954200	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:75946200-75954200	Weak transcription	Fetal Thymus	thymus
31	chr5:75946200-75954400	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr5:75946200-75954400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr5:75946200-75954400	Weak transcription	Primary B cells from peripheral blood	blood
34	chr5:75946200-75976000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr5:75946400-76001000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr5:75946600-75975000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr5:75946800-75953000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr5:75947000-75950400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr5:75947000-75970600	Weak transcription	Small Intestine	intestine
40	chr5:75947800-75981800	Strong transcription	Primary T cells from cord blood	blood
41	chr5:75947800-75992000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:75948000-75949200	Strong transcription	HepG2	liver
43	chr5:75948000-75952200	Strong transcription	Primary hematopoietic stem cells	blood
44	chr5:75948000-75976200	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr5:75948000-75976200	Strong transcription	Primary T helper cells fromperipheralblood	blood
46	chr5:75948000-75976400	Strong transcription	Placenta	Placenta
47	chr5:75948000-76004600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr5:75948200-75949200	Enhancers	GM12878-XiMat	blood
49	chr5:75948200-75949400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr5:75948400-75949600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

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