Variant report

Variant	rs1489192
Chromosome Location	chr11:46509344-46509345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:46503497..46505535-chr11:46508145..46510942,2	MCF-7	breast:
2	chr11:46507863..46510166-chr11:46511411..46513736,3	MCF-7	breast:

Extended variants
information (count: 105 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

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[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838602	0.98[EUR][1000 genomes];1.00[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[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038900	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11038906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038914	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];0.98[EUR][1000 genomes];1.00[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[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038927	0.94[EUR][1000 genomes];0.94[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[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12272795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12283172	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12292425	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]
rs12295266	0.91[EUR][1000 genomes];0.94[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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12574250	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12574259	0.93[CEU][hapmap];0.82[GIH][hapmap];0.96[TSI][hapmap]
rs12574668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12575519	0.96[EUR][1000 genomes]
rs12576115	0.92[EUR][1000 genomes]
rs12576317	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12576359	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12577142	0.94[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[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1472001	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];0.94[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[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17197116	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2046768	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs2067482	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2171667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2171668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279465	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.96[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[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2864072	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2864076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2902858	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34406563	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs35324223	0.84[EUR][1000 genomes]
rs35623865	1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3740974	0.96[EUR][1000 genomes]
rs3740977	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.95[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[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809047	0.85[CHD][hapmap];0.85[JPT][hapmap]
rs4307676	0.86[EUR][1000 genomes]
rs4319473	0.85[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap]
rs55657382	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55661562	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55750336	0.97[ASN][1000 genomes]
rs57535407	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58147945	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59319338	0.94[EUR][1000 genomes]
rs60722866	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60932698	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882674	0.81[EUR][1000 genomes]
rs61882678	0.88[EUR][1000 genomes]
rs61882682	0.94[EUR][1000 genomes]
rs61882683	0.92[EUR][1000 genomes]
rs61882691	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882701	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61882702	0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61882706	0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61882709	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882710	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882711	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882712	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882720	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882743	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882746	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882748	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882750	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882756	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61882757	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61882758	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61884262	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61884264	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61884271	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61884273	0.86[EUR][1000 genomes]
rs61884274	0.86[EUR][1000 genomes]
rs6485682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6485685	0.89[EUR][1000 genomes]
rs7108770	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7109698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap]
rs7112229	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7122039	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.82[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[TSI][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7126316	0.84[EUR][1000 genomes]
rs7126343	0.86[EUR][1000 genomes]
rs7127529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7128092	0.85[EUR][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[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73449983	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7481312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7484002	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs756343	0.97[ASN][1000 genomes]
rs7924401	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7930103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7932866	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]
rs7936413	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs7946705	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7951579	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7951870	1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs876701	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1489192	ATG13	cis	parietal	SCAN
rs1489192	C11orf49	cis	parietal	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46456800-46515000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
2	chr11:46464200-46513000	Weak transcription	Primary hematopoietic stem cells	blood
3	chr11:46465000-46513400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr11:46465600-46511200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr11:46479000-46513400	Weak transcription	Spleen	Spleen
6	chr11:46479000-46525600	Weak transcription	Lung	lung
7	chr11:46485600-46511200	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr11:46486000-46511400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:46486000-46511400	Weak transcription	HSMMtube	muscle
10	chr11:46486200-46513200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:46486200-46525800	Weak transcription	Fetal Brain Female	brain
12	chr11:46486400-46513600	Weak transcription	Esophagus	oesophagus
13	chr11:46486600-46518800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr11:46487000-46511400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr11:46487400-46514200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr11:46487600-46513600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr11:46487600-46514200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr11:46487600-46515000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:46488000-46511400	Weak transcription	Gastric	stomach
20	chr11:46488200-46513400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr11:46488200-46515000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr11:46489600-46511000	Weak transcription	Colon Smooth Muscle	Colon
23	chr11:46489600-46512000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr11:46490000-46511200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr11:46490000-46512000	Weak transcription	Adipose Nuclei	Adipose
26	chr11:46490000-46512400	Weak transcription	Stomach Smooth Muscle	stomach
27	chr11:46490200-46511200	Weak transcription	Placenta	Placenta
28	chr11:46490200-46525800	Weak transcription	Aorta	Aorta
29	chr11:46490400-46511200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:46490600-46511200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr11:46492800-46511400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr11:46492800-46511400	Weak transcription	HSMM	muscle
33	chr11:46492800-46513400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr11:46494000-46511400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr11:46494400-46511000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:46494400-46513600	Weak transcription	Brain Angular Gyrus	brain
37	chr11:46494400-46515000	Weak transcription	NH-A	brain
38	chr11:46494600-46511000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr11:46494600-46511400	Weak transcription	Liver	Liver
40	chr11:46494800-46515000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr11:46494800-46519800	Weak transcription	Psoas Muscle	Psoas
42	chr11:46495000-46511200	Weak transcription	K562	blood
43	chr11:46495000-46512000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr11:46495000-46512200	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr11:46495200-46512200	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr11:46495200-46514800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr11:46497200-46512000	Weak transcription	Primary B cells from peripheral blood	blood
48	chr11:46497600-46512000	Weak transcription	NHEK	skin
49	chr11:46497600-46537600	Weak transcription	A549	lung
50	chr11:46497800-46510800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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