Variant report

Variant	rs3825403
Chromosome Location	chr12:48457159-48457160
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10492082	0.80[ASN][1000 genomes]
rs1049392	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs10747529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875726	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10875727	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10875733	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10875739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875741	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10875744	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10875752	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs10875754	0.85[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap]
rs10875761	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs10875766	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11168350	0.94[JPT][hapmap]
rs11168353	1.00[JPT][hapmap]
rs11168354	1.00[JPT][hapmap]
rs11168358	1.00[JPT][hapmap]
rs11168363	0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11168364	0.95[CHD][hapmap];1.00[JPT][hapmap]
rs11168373	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs11168378	0.90[ASN][1000 genomes]
rs11168404	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11168417	0.86[CHD][hapmap];1.00[JPT][hapmap]
rs11168424	1.00[JPT][hapmap]
rs11168434	1.00[JPT][hapmap]
rs11168435	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs11168438	1.00[JPT][hapmap]
rs11168445	1.00[JPT][hapmap]
rs11168448	1.00[JPT][hapmap]
rs11168453	1.00[JPT][hapmap]
rs11168454	1.00[JPT][hapmap]
rs11832455	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11834818	0.93[ASN][1000 genomes]
rs12422355	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12423250	0.94[JPT][hapmap]
rs12426981	0.93[ASN][1000 genomes]
rs17122567	1.00[JPT][hapmap]
rs1859440	0.85[ASN][1000 genomes]
rs1859443	0.94[JPT][hapmap]
rs1978161	1.00[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.89[MEX][hapmap];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2107640	0.90[ASN][1000 genomes]
rs2158515	0.96[CEU][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2240306	0.81[ASN][1000 genomes]
rs2286020	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs2408954	1.00[JPT][hapmap]
rs3742075	0.90[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs4258439	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760678	0.92[ASN][1000 genomes]
rs56129148	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59667534	0.80[ASN][1000 genomes]
rs6580658	0.80[JPT][hapmap]
rs7138917	0.96[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299704	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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7302354	1.00[JPT][hapmap]
rs7303677	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7304428	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs733592	0.85[ASN][1000 genomes]
rs7484942	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs765260	0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.85[MEX][hapmap];0.86[ASN][1000 genomes]
rs7962390	1.00[JPT][hapmap]
rs7962569	0.94[JPT][hapmap]
rs8181670	0.81[CHD][hapmap];1.00[JPT][hapmap]
rs886589	0.90[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs954326	0.94[JPT][hapmap]
rs9651981	0.94[JPT][hapmap]
rs9804751	0.94[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs3825403	RP1-228P16.1	cis	Esophagus Muscularis	GTEx
rs3825403	C12orf41	cis	parietal	SCAN
rs3825403	SENP1	cis	parietal	SCAN
rs3825403	RP1-228P16.1	cis	Thyroid	GTEx
rs3825403	ZNF641	cis	Whole Blood	GTEx
rs3825403	RPAP3	cis	cerebellum	SCAN
rs3825403	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432000-48463400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
4	chr12:48435400-48457200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:48439200-48468000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr12:48440000-48457200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
9	chr12:48441600-48468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:48444200-48474600	Weak transcription	Gastric	stomach
12	chr12:48444800-48468000	Weak transcription	Spleen	Spleen
13	chr12:48449400-48464400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr12:48452000-48460200	Strong transcription	Hela-S3	cervix
15	chr12:48452000-48468600	Strong transcription	HUES48 Cell Line	embryonic stem cell
16	chr12:48452000-48468800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr12:48452000-48468800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr12:48452000-48469400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr12:48452200-48459600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr12:48452200-48459600	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr12:48452200-48459600	Strong transcription	NHDF-Ad	bronchial
22	chr12:48452200-48460000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr12:48452200-48460600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr12:48452200-48461200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr12:48452200-48461600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:48452200-48468600	Strong transcription	NH-A	brain
27	chr12:48452200-48468800	Strong transcription	HUES6 Cell Line	embryonic stem cell
28	chr12:48452200-48469000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr12:48452200-48469600	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr12:48452200-48470000	Strong transcription	Placenta	Placenta
31	chr12:48452400-48459400	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:48452400-48459600	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr12:48452400-48459600	Strong transcription	Rectal Mucosa Donor 31	rectum
34	chr12:48452400-48459600	Strong transcription	Osteobl	bone
35	chr12:48452400-48459800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr12:48452400-48460000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:48452400-48460600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:48452400-48460600	Strong transcription	Left Ventricle	heart
39	chr12:48452400-48461400	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:48452400-48461600	Strong transcription	Fetal Intestine Large	intestine
41	chr12:48452400-48463200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr12:48452400-48468800	Strong transcription	Adipose Nuclei	Adipose
43	chr12:48452400-48468800	Strong transcription	Duodenum Mucosa	Duodenum
44	chr12:48452400-48468800	Strong transcription	Fetal Thymus	thymus
45	chr12:48452400-48469600	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:48452600-48468400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr12:48452800-48458000	Strong transcription	NHEK	skin
48	chr12:48452800-48460000	Strong transcription	HepG2	liver
49	chr12:48452800-48461600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr12:48452800-48468000	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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