Variant report

Variant	rs3825184
Chromosome Location	chr12:49298340-49298341
allele	C/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	MXI1	chr12:49297738-49298477	SK-N-SH	brain:	n/a	n/a
2	CTCF	chr12:49296905-49298557	A549	lung:	n/a	n/a
3	MXI1	chr12:49297748-49298477	IMR90	lung:	n/a	n/a
4	TCF12	chr12:49297553-49298642	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:49207912..49209568-chr12:49296260..49299188,2	K562	blood:
2	chr12:49258108..49259713-chr12:49297461..49298990,2	MCF-7	breast:
3	chr12:49258556..49260730-chr12:49298046..49299547,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000239617	TF binding region
ENSG00000172602	Chromatin interaction
ENSG00000167535	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs1051886	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs1054376	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10747556	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs10747557	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs10747558	0.95[CHB][hapmap];0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs10783289	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10783290	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10783292	0.94[ASN][1000 genomes]
rs10783293	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783294	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.99[ASN][1000 genomes]
rs10783295	0.99[ASN][1000 genomes]
rs10783297	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875883	0.83[CHB][hapmap];0.89[CHD][hapmap]
rs10875885	0.82[CHB][hapmap]
rs10875886	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875888	0.88[ASN][1000 genomes]
rs10875893	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.97[ASN][1000 genomes]
rs10875894	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10875895	0.99[ASN][1000 genomes]
rs10875896	0.91[ASN][1000 genomes]
rs10875897	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs10875898	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10875900	0.90[ASN][1000 genomes]
rs10875901	0.89[ASN][1000 genomes]
rs10875902	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs1111662	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];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11168779	0.99[ASN][1000 genomes]
rs11168783	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.99[ASN][1000 genomes]
rs11168784	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11168785	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.99[ASN][1000 genomes]
rs11168790	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.99[ASN][1000 genomes]
rs11168792	0.97[ASN][1000 genomes]
rs11168794	0.97[ASN][1000 genomes]
rs11168795	0.90[ASN][1000 genomes]
rs11168797	0.91[ASN][1000 genomes]
rs11168798	0.84[ASN][1000 genomes]
rs11168800	0.84[ASN][1000 genomes]
rs11168801	0.84[ASN][1000 genomes]
rs11168803	0.90[ASN][1000 genomes]
rs11168812	0.89[ASN][1000 genomes]
rs11608916	0.98[ASN][1000 genomes]
rs11610459	0.99[ASN][1000 genomes]
rs11610497	0.99[ASN][1000 genomes]
rs11614474	0.99[ASN][1000 genomes]
rs12227240	0.97[ASN][1000 genomes]
rs12228521	0.99[ASN][1000 genomes]
rs12229275	0.94[ASN][1000 genomes]
rs12423542	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[ASN][1000 genomes]
rs12579249	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1318692	1.00[ASN][1000 genomes]
rs1690182	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1818996	0.90[ASN][1000 genomes]
rs1830192	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2030900	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2070940	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2073480	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.91[ASN][1000 genomes]
rs2131713	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs2272311	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs2272312	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2293449	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs2368701	0.99[ASN][1000 genomes]
rs2453063	0.90[ASN][1000 genomes]
rs2463175	0.88[ASN][1000 genomes]
rs2641450	0.86[ASN][1000 genomes]
rs2694839	0.88[ASN][1000 genomes]
rs2694840	0.87[ASN][1000 genomes]
rs3741627	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs3759146	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[ASN][1000 genomes]
rs3782353	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs3809147	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];1.00[ASN][1000 genomes]
rs3825182	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.97[ASN][1000 genomes]
rs4018510	0.90[ASN][1000 genomes]
rs4237854	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4433614	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4526804	0.89[ASN][1000 genomes]
rs4760600	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.98[ASN][1000 genomes]
rs4760661	0.98[ASN][1000 genomes]
rs4760662	0.82[CHD][hapmap]
rs4760663	0.82[CHB][hapmap];0.86[CHD][hapmap];0.81[ASN][1000 genomes]
rs4760664	0.89[ASN][1000 genomes]
rs4760665	0.99[ASN][1000 genomes]
rs4760666	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.90[ASN][1000 genomes]
rs4760667	0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4760668	0.90[ASN][1000 genomes]
rs58023472	0.99[ASN][1000 genomes]
rs59087236	0.89[ASN][1000 genomes]
rs61941142	0.99[ASN][1000 genomes]
rs61942166	0.89[ASN][1000 genomes]
rs61942167	0.91[ASN][1000 genomes]
rs61942169	0.90[ASN][1000 genomes]
rs61942207	0.89[ASN][1000 genomes]
rs61942209	0.80[ASN][1000 genomes]
rs6580696	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs7297958	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7298330	0.99[ASN][1000 genomes]
rs7304942	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7313988	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7489036	0.95[ASN][1000 genomes]
rs7963018	0.90[ASN][1000 genomes]
rs7963160	0.88[ASN][1000 genomes]
rs7976473	0.85[ASN][1000 genomes]
rs833820	0.95[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.88[ASN][1000 genomes]
rs833821	0.88[ASN][1000 genomes]
rs833822	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs833827	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs833828	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs833839	0.83[ASN][1000 genomes]
rs833840	0.86[CHB][hapmap];0.86[CHD][hapmap];0.81[JPT][hapmap];0.83[ASN][1000 genomes]
rs833841	0.86[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.82[ASN][1000 genomes]
rs833842	0.82[ASN][1000 genomes]
rs833843	0.86[CHB][hapmap];0.86[CHD][hapmap];0.83[MEX][hapmap]
rs961320	1.00[ASN][1000 genomes]
rs9645813	0.83[ASN][1000 genomes]
rs9783452	0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.89[ASN][1000 genomes]
rs9783477	0.89[ASN][1000 genomes]
rs9788029	0.94[ASN][1000 genomes]
rs9795742	0.97[ASN][1000 genomes]
rs9796008	0.99[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	nsv832404	chr12:49258560-49458555	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3825184	RP11-302B13.1	cis	Whole Blood	GTEx
rs3825184	WNT10B	cis	parietal	SCAN
rs3825184	FKBP11	cis	cerebellum	SCAN
rs3825184	FKBP11	cis	parietal	SCAN
rs3825184	AQP2	cis	parietal	SCAN

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49297200-49298400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
2	chr12:49297200-49298400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr12:49297200-49298400	Active TSS	Brain Substantia Nigra	brain
4	chr12:49297400-49298400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:49297400-49298400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr12:49297400-49298400	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr12:49297400-49298400	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr12:49297600-49298400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr12:49297600-49298400	Active TSS	Duodenum Mucosa	Duodenum
10	chr12:49297600-49298400	Active TSS	A549	lung
11	chr12:49297800-49298400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
12	chr12:49297800-49298400	Active TSS	H1 Cell Line	embryonic stem cell
13	chr12:49297800-49298400	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr12:49297800-49298400	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr12:49297800-49298400	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr12:49297800-49298400	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr12:49297800-49298400	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr12:49297800-49298400	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr12:49297800-49298400	Flanking Active TSS	Primary hematopoietic stem cells	blood
20	chr12:49297800-49298400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr12:49297800-49298400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
22	chr12:49297800-49298400	Flanking Active TSS	Adipose Nuclei	Adipose
23	chr12:49297800-49298400	Active TSS	Brain Hippocampus Middle	brain
24	chr12:49297800-49298400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
25	chr12:49297800-49298400	Active TSS	Fetal Kidney	kidney
26	chr12:49297800-49298400	Active TSS	Fetal Lung	lung
27	chr12:49297800-49298400	Flanking Active TSS	Fetal Muscle Trunk	muscle
28	chr12:49297800-49298400	Flanking Active TSS	Fetal Muscle Leg	muscle
29	chr12:49297800-49298400	Active TSS	Rectal Smooth Muscle	rectum
30	chr12:49297800-49298400	Flanking Active TSS	HepG2	liver
31	chr12:49297800-49298400	Active TSS	HSMM	muscle
32	chr12:49297800-49298400	Bivalent/Poised TSS	NHEK	skin
33	chr12:49297800-49298600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:49297800-49298600	Active TSS	Brain Angular Gyrus	brain
35	chr12:49298000-49298400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:49298000-49298400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:49298000-49298400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr12:49298000-49298400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:49298000-49298400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:49298000-49298400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr12:49298000-49298400	Flanking Active TSS	Brain Anterior Caudate	brain
42	chr12:49298000-49298400	Enhancers	Lung	lung
43	chr12:49298000-49298400	Flanking Active TSS	Pancreas	Pancrea
44	chr12:49298000-49298400	Flanking Active TSS	Right Atrium	heart
45	chr12:49298000-49298400	Enhancers	Stomach Mucosa	stomach
46	chr12:49298000-49298400	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
47	chr12:49298000-49298400	Enhancers	Spleen	Spleen
48	chr12:49298000-49298400	Enhancers	HMEC	breast
49	chr12:49298000-49298400	Flanking Active TSS	NH-A	brain
50	chr12:49298000-49298600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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