Variant report

Variant	rs2959097
Chromosome Location	chr11:46007377-46007378
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45938159..45940217-chr11:46005267..46008166,2	MCF-7	breast:
2	chr11:45998746..46001549-chr11:46002921..46008009,7	K562	blood:
3	chr11:45997750..46001916-chr11:46003160..46008009,7	K562	blood:

Variant related genes	Relation type
ENSG00000121680	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1024004	1.00[CHB][hapmap]
rs1038733	1.00[CEU][hapmap]
rs10742773	1.00[CEU][hapmap];0.96[YRI][hapmap];0.95[EUR][1000 genomes]
rs10769177	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10838537	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10838558	1.00[CEU][hapmap]
rs10838564	1.00[CEU][hapmap]
rs11820849	1.00[CEU][hapmap]
rs11820877	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11827687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11828167	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1401420	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1401421	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1490087	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs1565412	1.00[CEU][hapmap]
rs16938429	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16938437	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1907003	1.00[CEU][hapmap]
rs1973721	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1994599	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2013010	1.00[CEU][hapmap]
rs2130469	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs2130471	1.00[CEU][hapmap]
rs2171895	1.00[CEU][hapmap]
rs2860376	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2860433	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2863714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes]
rs2932510	1.00[CEU][hapmap]
rs2932512	1.00[CEU][hapmap]
rs2932515	1.00[CEU][hapmap]
rs2932516	1.00[CEU][hapmap]
rs2945996	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2945998	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2946000	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2946002	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2946005	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2946008	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2946009	1.00[CEU][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2959082	1.00[CEU][hapmap]
rs2959083	1.00[CEU][hapmap]
rs2959085	1.00[CEU][hapmap]
rs2959088	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2959089	0.84[EUR][1000 genomes]
rs2959095	1.00[CEU][hapmap];0.81[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2959096	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2959103	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2959104	1.00[CEU][hapmap]
rs3107239	0.80[AFR][1000 genomes]
rs3929339	1.00[CEU][hapmap]
rs4237661	1.00[CEU][hapmap]
rs4756042	1.00[CEU][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4756043	0.94[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4756048	1.00[CEU][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4756056	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4756057	1.00[CEU][hapmap]
rs4756058	1.00[CEU][hapmap]
rs4756059	1.00[CEU][hapmap]
rs55945697	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61652532	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61882508	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61882509	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61882510	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61882511	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61882513	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61882514	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61882534	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61882535	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61882536	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61882538	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61882539	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61882540	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61882541	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61882542	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6485660	1.00[CEU][hapmap]
rs6485663	1.00[CEU][hapmap]
rs6485664	1.00[CEU][hapmap]
rs7103299	1.00[CEU][hapmap]
rs7106689	1.00[CEU][hapmap]
rs7120227	1.00[CEU][hapmap]
rs7129942	1.00[CEU][hapmap]
rs7130282	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73452216	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7397035	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7924996	1.00[CEU][hapmap]
rs7932895	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7934407	1.00[CEU][hapmap]
rs7934572	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7934681	1.00[CEU][hapmap];0.92[YRI][hapmap];0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7937896	1.00[CEU][hapmap]
rs7942083	1.00[CEU][hapmap]
rs7942246	1.00[CEU][hapmap]
rs7946524	1.00[CEU][hapmap]
rs923531	1.00[CHB][hapmap]
rs939106	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][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	nsv523952	chr11:45983385-46028281	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
2	nsv972947	chr11:46004497-46007589	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:45993000-46015000	Weak transcription	Psoas Muscle	Psoas
2	chr11:45993000-46017600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr11:46000400-46013000	Weak transcription	Fetal Intestine Large	intestine
4	chr11:46000600-46010400	Weak transcription	Hela-S3	cervix
5	chr11:46000800-46010200	Weak transcription	Liver	Liver
6	chr11:46000800-46012400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr11:46001000-46015400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:46001400-46013200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr11:46001400-46013600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr11:46001400-46015200	Weak transcription	Pancreas	Pancrea
11	chr11:46001400-46016000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr11:46001400-46070400	Weak transcription	Primary hematopoietic stem cells	blood
13	chr11:46001600-46015200	Weak transcription	Fetal Muscle Trunk	muscle
14	chr11:46001600-46015400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr11:46001600-46016400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr11:46001600-46021000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr11:46002000-46015000	Weak transcription	Fetal Muscle Leg	muscle
18	chr11:46002000-46025000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr11:46002000-46042400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr11:46002000-46056200	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:46002200-46024800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr11:46002200-46025000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr11:46002600-46012000	Weak transcription	GM12878-XiMat	blood
24	chr11:46002600-46023200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr11:46004000-46007600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:46004600-46007800	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr11:46004600-46012400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:46004800-46007800	Weak transcription	Gastric	stomach
29	chr11:46004800-46009200	Weak transcription	Fetal Kidney	kidney
30	chr11:46004800-46011200	Weak transcription	HUVEC	blood vessel
31	chr11:46004800-46015000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr11:46005000-46012000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:46005000-46012000	Weak transcription	Ovary	ovary
34	chr11:46005000-46014400	Weak transcription	Fetal Stomach	stomach
35	chr11:46005200-46008800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr11:46005200-46012000	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr11:46005200-46014800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr11:46005200-46014800	Weak transcription	NHLF	lung
39	chr11:46005200-46015000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr11:46005400-46008800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:46005400-46009200	Weak transcription	HSMMtube	muscle
42	chr11:46005400-46014400	Weak transcription	Aorta	Aorta
43	chr11:46005400-46014400	Weak transcription	Fetal Lung	lung
44	chr11:46005400-46014800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr11:46005400-46014800	Weak transcription	NH-A	brain
46	chr11:46005400-46015200	Weak transcription	Left Ventricle	heart
47	chr11:46005400-46015200	Weak transcription	Right Ventricle	heart
48	chr11:46005600-46012400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr11:46005600-46014600	Weak transcription	Colon Smooth Muscle	Colon
50	chr11:46006000-46015200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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