Variant report

Variant	rs11169101
Chromosome Location	chr12:50068809-50068810
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50067511..50069369-chr12:50073170..50075270,2	K562	blood:
2	chr12:50065718..50069326-chr12:50125302..50127957,3	K562	blood:
3	chr12:50062633..50068951-chr12:50134385..50140154,8	K562	blood:
4	chr12:50066343..50069112-chr12:50133509..50136690,4	MCF-7	breast:
5	chr12:50067484..50070430-chr12:50082743..50084854,2	K562	blood:
6	chr12:50048532..50051602-chr12:50065327..50069233,3	K562	blood:
7	chr12:50067389..50069514-chr12:50096557..50099355,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1049986	0.85[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10875964	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10875968	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169063	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11169065	1.00[JPT][hapmap]
rs11169069	0.86[JPT][hapmap]
rs11169073	0.85[JPT][hapmap]
rs11169080	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11169081	0.85[JPT][hapmap]
rs11169082	0.85[JPT][hapmap]
rs11169092	0.85[JPT][hapmap]
rs11169097	0.85[JPT][hapmap];0.80[YRI][hapmap];0.89[AMR][1000 genomes]
rs11169104	0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169106	0.85[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169109	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169111	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169112	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169113	0.81[AMR][1000 genomes]
rs11169118	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169125	0.85[AMR][1000 genomes]
rs11169127	0.83[AMR][1000 genomes]
rs11169133	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs11169140	0.91[CEU][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1150057	1.00[JPT][hapmap]
rs11615488	0.97[ASN][1000 genomes]
rs11833411	0.85[JPT][hapmap]
rs11834380	0.85[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12296586	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12299505	0.85[JPT][hapmap];0.80[YRI][hapmap];0.83[AMR][1000 genomes]
rs12299513	0.83[AMR][1000 genomes]
rs12301824	0.90[ASN][1000 genomes]
rs12303310	0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12304796	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12305460	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12308256	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12309940	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12310510	0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12311839	0.86[JPT][hapmap]
rs12314795	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12315224	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12315791	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12316284	0.85[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12317646	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12321169	0.85[AMR][1000 genomes]
rs12321819	0.85[JPT][hapmap]
rs13906	0.86[JPT][hapmap]
rs1470906	0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1574326	0.85[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17123808	0.85[JPT][hapmap]
rs17123865	0.89[CEU][hapmap]
rs17123981	0.91[CEU][hapmap];0.93[YRI][hapmap]
rs1902329	1.00[JPT][hapmap]
rs1902330	0.82[JPT][hapmap]
rs2278068	1.00[JPT][hapmap]
rs2278069	0.85[JPT][hapmap]
rs2303305	0.85[JPT][hapmap]
rs2336058	0.85[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2878532	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3815832	0.85[JPT][hapmap]
rs3887727	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3887728	0.85[JPT][hapmap]
rs4073998	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4133070	0.85[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4563	0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4584654	0.85[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57191490	0.87[ASN][1000 genomes]
rs57342147	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs57463238	0.81[AMR][1000 genomes]
rs58446833	0.83[AMR][1000 genomes]
rs59233136	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59849800	0.83[AMR][1000 genomes]
rs60121503	0.87[ASN][1000 genomes]
rs60402517	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs61512987	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61616163	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61620972	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61710637	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6580719	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7131915	0.86[JPT][hapmap]
rs7132792	0.85[JPT][hapmap]
rs7136052	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7137976	0.85[JPT][hapmap];0.83[YRI][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7296281	0.86[JPT][hapmap]
rs7299002	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7299609	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7301209	0.86[JPT][hapmap]
rs7306877	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7309607	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7312658	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7313738	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73305085	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs73305098	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73306808	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73309030	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs74089182	0.87[ASN][1000 genomes]
rs7688	0.85[JPT][hapmap];0.83[YRI][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7952734	0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7952938	0.82[ASN][1000 genomes]
rs7953911	0.85[JPT][hapmap]
rs7954994	0.85[JPT][hapmap];0.86[YRI][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7955586	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7956089	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7956181	0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7962645	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7962863	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7963954	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7965658	1.00[JPT][hapmap]
rs7967624	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7970241	0.85[JPT][hapmap]
rs7973389	0.85[JPT][hapmap]
rs7975599	0.85[JPT][hapmap]
rs7975712	1.00[CHB][hapmap]
rs7977389	0.85[JPT][hapmap]
rs7979262	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7979285	0.83[CEU][hapmap];0.88[JPT][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7980979	0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8626	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs876889	0.85[JPT][hapmap]
rs897056	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9804749	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs9804971	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50054400-50069800	Enhancers	Left Ventricle	heart
2	chr12:50060400-50069400	Enhancers	Fetal Thymus	thymus
3	chr12:50062000-50069600	Enhancers	Primary B cells from peripheral blood	blood
4	chr12:50063200-50069200	Enhancers	Thymus	Thymus
5	chr12:50063200-50069400	Enhancers	Lung	lung
6	chr12:50063200-50069800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:50063600-50069200	Enhancers	Primary hematopoietic stem cells	blood
8	chr12:50063600-50069400	Enhancers	Right Atrium	heart
9	chr12:50063800-50069400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr12:50063800-50069400	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr12:50063800-50069400	Enhancers	Right Ventricle	heart
12	chr12:50063800-50070000	Enhancers	Psoas Muscle	Psoas
13	chr12:50063800-50070200	Enhancers	Ovary	ovary
14	chr12:50063800-50070600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr12:50063800-50070600	Enhancers	Fetal Lung	lung
16	chr12:50064200-50070000	Enhancers	Fetal Muscle Leg	muscle
17	chr12:50064400-50069400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:50064400-50069400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:50064400-50069400	Enhancers	Stomach Mucosa	stomach
20	chr12:50064400-50069600	Enhancers	Placenta	Placenta
21	chr12:50064600-50069000	Enhancers	NH-A	brain
22	chr12:50064600-50069400	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr12:50064600-50069600	Enhancers	Small Intestine	intestine
24	chr12:50064600-50070200	Enhancers	Fetal Heart	heart
25	chr12:50064600-50070200	Enhancers	Fetal Stomach	stomach
26	chr12:50065000-50069000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:50065000-50069400	Enhancers	Fetal Intestine Large	intestine
28	chr12:50065200-50069400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr12:50065200-50069400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:50065200-50069400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:50065200-50069800	Enhancers	Fetal Muscle Trunk	muscle
32	chr12:50065400-50069200	Enhancers	Fetal Intestine Small	intestine
33	chr12:50065400-50069400	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr12:50065400-50069600	Enhancers	Primary T cells fromperipheralblood	blood
35	chr12:50065600-50070000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:50065600-50070600	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr12:50065600-50071600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr12:50065800-50069000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr12:50065800-50069200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
40	chr12:50065800-50069200	Enhancers	HUVEC	blood vessel
41	chr12:50065800-50069400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:50065800-50071200	Enhancers	Primary T killer memory cells from peripheral blood	blood
43	chr12:50065800-50071600	Enhancers	Primary T cells from cord blood	blood
44	chr12:50066000-50069200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr12:50066000-50069800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:50066200-50069000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr12:50066200-50069200	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr12:50066200-50069400	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr12:50066200-50069600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:50066400-50069000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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