Variant report

Variant	rs12292425
Chromosome Location	chr11:46644143-46644144
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 112 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10160701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10838602	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11038897	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs11038900	0.90[EUR][1000 genomes]
rs11038906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11038914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11038919	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[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11038927	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11819869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12272795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12283172	0.92[EUR][1000 genomes]
rs12295266	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12573978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12574250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs12574259	0.93[CEU][hapmap];0.82[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs12574668	0.89[EUR][1000 genomes]
rs12574918	0.81[EUR][1000 genomes]
rs12575519	0.90[EUR][1000 genomes]
rs12576115	0.87[EUR][1000 genomes]
rs12576317	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12576359	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12577142	0.89[EUR][1000 genomes]
rs12578042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1472001	0.83[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.90[EUR][1000 genomes]
rs1489192	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16938506	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17197116	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2046768	0.92[EUR][1000 genomes]
rs2067482	0.92[EUR][1000 genomes]
rs2171667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs2171668	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[TSI][hapmap];0.92[EUR][1000 genomes]
rs2279465	0.92[EUR][1000 genomes]
rs2291487	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2864072	0.92[EUR][1000 genomes]
rs2864076	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs2902858	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[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34406563	0.88[EUR][1000 genomes]
rs35324223	0.80[EUR][1000 genomes]
rs35623865	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3740974	0.92[EUR][1000 genomes]
rs3740977	0.91[EUR][1000 genomes]
rs3802888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4307676	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4319473	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs4423142	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55657382	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55661562	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55896955	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56349329	0.85[EUR][1000 genomes]
rs57535407	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs57739486	0.81[EUR][1000 genomes]
rs57744667	0.85[EUR][1000 genomes]
rs58147945	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59319338	0.89[EUR][1000 genomes]
rs60722866	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60932698	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882678	0.84[EUR][1000 genomes]
rs61882682	0.90[EUR][1000 genomes]
rs61882683	0.85[EUR][1000 genomes]
rs61882691	0.92[EUR][1000 genomes]
rs61882701	0.92[EUR][1000 genomes]
rs61882702	0.92[EUR][1000 genomes]
rs61882706	0.91[EUR][1000 genomes]
rs61882709	0.92[EUR][1000 genomes]
rs61882710	0.92[EUR][1000 genomes]
rs61882711	0.92[EUR][1000 genomes]
rs61882712	0.90[EUR][1000 genomes]
rs61882720	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882743	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882746	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882748	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882750	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882756	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882757	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882758	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61884262	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884264	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884271	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884273	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61884274	0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61884292	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61884295	0.85[EUR][1000 genomes]
rs61884301	0.80[EUR][1000 genomes]
rs6485682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs6485685	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7108770	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7109698	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[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7112229	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs7122039	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[TSI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7125907	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];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7126316	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7126343	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7127529	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[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7128092	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7130141	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73449983	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7481312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7484002	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7924401	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7926389	0.93[CEU][hapmap];0.83[EUR][1000 genomes]
rs7930103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs7932866	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs7936413	0.92[EUR][1000 genomes]
rs7946705	0.92[EUR][1000 genomes]
rs7951579	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs7951870	0.91[EUR][1000 genomes]
rs876701	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044225	chr11:46472580-46771102	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv541030	chr11:46472580-46771102	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1046990	chr11:46501436-46669636	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv541031	chr11:46501436-46669636	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv897321	chr11:46515902-46673344	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12292425	DKFZp779M0652	cis	parietal	SCAN
rs12292425	ATG13	cis	parietal	SCAN
rs12292425	PROX1	trans	cerebellum	SCAN
rs12292425	C11orf49	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46639800-46645600	Weak transcription	Aorta	Aorta
2	chr11:46640000-46644200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr11:46640000-46651400	Weak transcription	Gastric	stomach
4	chr11:46640000-46664200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:46640000-46670800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr11:46640200-46651800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:46640600-46645800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr11:46640600-46646200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr11:46640600-46651200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr11:46640600-46651800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:46640600-46651800	Weak transcription	Fetal Brain Male	brain
12	chr11:46640600-46667200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:46640600-46667200	Weak transcription	Psoas Muscle	Psoas
14	chr11:46640800-46644200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr11:46640800-46645600	Weak transcription	Spleen	Spleen
16	chr11:46640800-46645600	Weak transcription	HSMMtube	muscle
17	chr11:46640800-46645800	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr11:46640800-46645800	Weak transcription	Colon Smooth Muscle	Colon
19	chr11:46640800-46645800	Weak transcription	Fetal Lung	lung
20	chr11:46640800-46645800	Weak transcription	HSMM	muscle
21	chr11:46640800-46646000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr11:46640800-46646000	Weak transcription	A549	lung
23	chr11:46640800-46646200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr11:46640800-46646400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr11:46640800-46646400	Weak transcription	Rectal Smooth Muscle	rectum
26	chr11:46640800-46646600	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr11:46640800-46646800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr11:46640800-46647000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr11:46640800-46649400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr11:46640800-46651400	Weak transcription	NHDF-Ad	bronchial
31	chr11:46640800-46651800	Weak transcription	Fetal Kidney	kidney
32	chr11:46640800-46652200	Weak transcription	Small Intestine	intestine
33	chr11:46640800-46652600	Weak transcription	NH-A	brain
34	chr11:46640800-46653400	Weak transcription	HUVEC	blood vessel
35	chr11:46640800-46664400	Weak transcription	GM12878-XiMat	blood
36	chr11:46640800-46670600	Weak transcription	Fetal Heart	heart
37	chr11:46640800-46670800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr11:46640800-46673000	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr11:46641000-46646800	Weak transcription	Brain Angular Gyrus	brain
40	chr11:46641000-46647200	Weak transcription	Hela-S3	cervix
41	chr11:46641000-46654400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr11:46641000-46657000	Strong transcription	Fetal Stomach	stomach
43	chr11:46641200-46645800	Weak transcription	Primary B cells from cord blood	blood
44	chr11:46641200-46647200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr11:46641200-46648800	Strong transcription	Fetal Thymus	thymus
46	chr11:46641200-46651800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr11:46641200-46651800	Weak transcription	Ovary	ovary
48	chr11:46641200-46653800	Weak transcription	HMEC	breast
49	chr11:46641400-46644400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr11:46641400-46647600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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