Variant report

Variant	rs2291487
Chromosome Location	chr11:46456344-46456345
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:46448640..46451542-chr11:46454493..46456535,2	K562	blood:
2	chr11:46450955..46452945-chr11:46454344..46456750,3	MCF-7	breast:
3	chr11:46437731..46440325-chr11:46455877..46458436,2	K562	blood:
4	chr11:46448640..46452068-chr11:46454493..46457739,3	K562	blood:

Variant related genes	Relation type
ENSG00000110497	Chromatin interaction
ENSG00000244313	Chromatin interaction

Extended variants
information (count: 104 )
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];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10838602	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038900	0.96[EUR][1000 genomes]
rs11038906	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11038919	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];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11038927	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11819869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12272795	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12283172	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];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12292425	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]
rs12295266	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12573978	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12574250	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12574668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12575519	0.96[EUR][1000 genomes]
rs12576115	0.95[EUR][1000 genomes]
rs12576317	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12576359	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12577142	0.95[EUR][1000 genomes]
rs12578042	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]
rs1472001	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489192	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]
rs16938506	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17197116	0.84[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.88[MKK][hapmap];0.88[YRI][hapmap];0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2046768	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2067482	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2171667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279465	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2864072	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2864076	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2902858	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]
rs34406563	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.96[TSI][hapmap];0.95[EUR][1000 genomes]
rs35324223	0.84[EUR][1000 genomes]
rs35623865	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs3740974	0.98[EUR][1000 genomes]
rs3740977	0.85[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes]
rs3802888	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]
rs3809047	0.85[JPT][hapmap]
rs4307676	0.87[EUR][1000 genomes]
rs55657382	0.91[EUR][1000 genomes]
rs55661562	0.91[EUR][1000 genomes]
rs55750336	0.90[ASN][1000 genomes]
rs55896955	0.80[EUR][1000 genomes]
rs57535407	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58147945	0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59319338	0.97[EUR][1000 genomes]
rs60722866	0.88[EUR][1000 genomes]
rs60932698	0.89[EUR][1000 genomes]
rs61882674	0.84[EUR][1000 genomes]
rs61882678	0.90[EUR][1000 genomes]
rs61882682	0.98[EUR][1000 genomes]
rs61882683	0.93[EUR][1000 genomes]
rs61882691	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61882701	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882702	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61882706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61882709	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882710	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882711	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882712	0.98[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882720	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882743	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882746	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882748	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882750	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61882756	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882757	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61882758	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61884262	0.85[EUR][1000 genomes]
rs61884264	0.91[EUR][1000 genomes]
rs61884271	0.89[EUR][1000 genomes]
rs61884273	0.87[EUR][1000 genomes]
rs61884274	0.87[EUR][1000 genomes]
rs61884292	0.80[EUR][1000 genomes]
rs6485682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6485685	0.91[EUR][1000 genomes]
rs7108770	0.89[EUR][1000 genomes]
rs7109698	0.81[EUR][1000 genomes]
rs7112229	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7122039	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]
rs7125907	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];0.82[ASN][1000 genomes]
rs7126316	0.86[EUR][1000 genomes]
rs7126343	0.87[EUR][1000 genomes]
rs7127529	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7128092	0.86[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[TSI][hapmap];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73449983	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7481312	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];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7484002	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];0.91[EUR][1000 genomes]
rs756343	0.90[ASN][1000 genomes]
rs7924401	0.92[EUR][1000 genomes]
rs7930103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7932866	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs7936413	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs7946705	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7951579	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7951870	1.00[CEU][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs876701	1.00[CEU][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]

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	nsv554202	chr11:46334239-46469900	Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv1050614	chr11:46414720-46496732	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv541029	chr11:46442658-46460232	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2291487	ATG13	cis	parietal	SCAN
rs2291487	C11orf49	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46417800-46463400	Weak transcription	Fetal Brain Male	brain
2	chr11:46426800-46468800	Weak transcription	Psoas Muscle	Psoas
3	chr11:46433600-46466400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr11:46436600-46466400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:46438000-46461400	Strong transcription	Primary T cells from cord blood	blood
6	chr11:46438400-46457200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:46438400-46459600	Strong transcription	Dnd41	blood
8	chr11:46440400-46466200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:46444000-46456600	Weak transcription	Fetal Heart	heart
10	chr11:46444800-46457200	Weak transcription	Small Intestine	intestine
11	chr11:46445800-46456600	Strong transcription	Duodenum Mucosa	Duodenum
12	chr11:46445800-46458000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:46447000-46457400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr11:46447200-46457600	Strong transcription	Fetal Stomach	stomach
15	chr11:46447600-46457600	Strong transcription	Liver	Liver
16	chr11:46447600-46457600	Strong transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:46447800-46460600	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr11:46448200-46457800	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr11:46448600-46457600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr11:46448800-46457600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr11:46448800-46457600	Strong transcription	Fetal Muscle Trunk	muscle
22	chr11:46449000-46456600	Strong transcription	Fetal Muscle Leg	muscle
23	chr11:46449000-46457400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr11:46449600-46457800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr11:46450000-46457400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr11:46450400-46458000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr11:46450600-46456800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:46450800-46456600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:46450800-46456800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:46450800-46457600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr11:46451000-46456600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr11:46451000-46456800	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr11:46451000-46457000	Strong transcription	Fetal Intestine Large	intestine
34	chr11:46451000-46457400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:46451000-46457400	Strong transcription	Primary T cells fromperipheralblood	blood
36	chr11:46451000-46457400	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:46451000-46457400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:46451000-46457600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr11:46451000-46457800	Strong transcription	HepG2	liver
40	chr11:46451000-46458000	Strong transcription	Placenta	Placenta
41	chr11:46451000-46459600	Strong transcription	Primary B cells from peripheral blood	blood
42	chr11:46451200-46457800	Strong transcription	Fetal Thymus	thymus
43	chr11:46451400-46456800	Strong transcription	Stomach Smooth Muscle	stomach
44	chr11:46451400-46467600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr11:46451600-46456400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:46451600-46459000	Strong transcription	Primary B cells from cord blood	blood
47	chr11:46451800-46457600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:46451800-46457600	Strong transcription	Aorta	Aorta
49	chr11:46452000-46456600	Strong transcription	Primary T killer memory cells from peripheral blood	blood
50	chr11:46452000-46456600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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