Variant report

Variant	rs1401421
Chromosome Location	chr11:46005829-46005830
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:45945921..45947947-chr11:46005632..46007133,2	K562	blood:
2	chr11:46000949..46006706-chr11:46011674..46018213,17	K562	blood:
3	chr11:45987934..45989618-chr11:46004381..46006271,2	K562	blood:
4	chr11:45938159..45940217-chr11:46005267..46008166,2	MCF-7	breast:
5	chr11:45998746..46001549-chr11:46002921..46008009,7	K562	blood:
6	chr11:45997750..46001916-chr11:46003160..46008009,7	K562	blood:

Variant related genes	Relation type
ENSG00000165905	Chromatin interaction
ENSG00000121680	Chromatin interaction

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10128629	1.00[ASN][1000 genomes]
rs1024004	1.00[CHB][hapmap]
rs1038733	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs10734539	1.00[ASN][1000 genomes]
rs10734540	1.00[ASN][1000 genomes]
rs10742773	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769177	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10838528	1.00[ASN][1000 genomes]
rs10838537	0.85[AFR][1000 genomes]
rs10838558	1.00[CEU][hapmap]
rs10838563	1.00[ASN][1000 genomes]
rs10838564	1.00[CEU][hapmap]
rs11038827	1.00[ASN][1000 genomes]
rs11820849	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11820877	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11827687	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11827732	1.00[ASN][1000 genomes]
rs11828167	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12292649	1.00[ASN][1000 genomes]
rs1401420	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1490082	1.00[ASN][1000 genomes]
rs1490087	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1565412	1.00[CEU][hapmap]
rs16938429	1.00[CEU][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16938437	1.00[CEU][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1907003	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs1973721	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1994599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2013010	1.00[CEU][hapmap]
rs2130469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2130470	1.00[ASN][1000 genomes]
rs2130471	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2130473	1.00[ASN][1000 genomes]
rs2171895	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2860376	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2860433	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2863714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28668543	1.00[ASN][1000 genomes]
rs2932510	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2932512	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2932515	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2932516	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2945996	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945998	1.00[CEU][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946000	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946002	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946008	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2946009	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959082	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2959083	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs2959085	1.00[CEU][hapmap]
rs2959088	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2959089	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959095	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959097	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]
rs2959103	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2959104	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs3929339	1.00[CEU][hapmap]
rs4237661	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs4281461	1.00[ASN][1000 genomes]
rs4756042	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756043	0.87[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs4756048	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4756057	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs4756058	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs4756059	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs55945697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56288505	1.00[ASN][1000 genomes]
rs61652532	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61882507	1.00[ASN][1000 genomes]
rs61882508	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882509	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882510	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882511	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882513	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882514	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882534	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882535	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882536	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882538	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882539	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882540	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882541	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882542	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61882543	1.00[ASN][1000 genomes]
rs61882544	1.00[ASN][1000 genomes]
rs61882545	1.00[ASN][1000 genomes]
rs61882546	1.00[ASN][1000 genomes]
rs61882547	1.00[ASN][1000 genomes]
rs61884152	1.00[ASN][1000 genomes]
rs6485660	1.00[CEU][hapmap]
rs6485663	1.00[CEU][hapmap]
rs6485664	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7103299	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7106689	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7111900	1.00[ASN][1000 genomes]
rs7120227	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7125387	1.00[ASN][1000 genomes]
rs7129942	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7130282	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73452216	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7397035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7478883	1.00[ASN][1000 genomes]
rs7924996	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7932895	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934407	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7934572	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7934681	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7937896	1.00[CEU][hapmap]
rs7942083	1.00[CEU][hapmap]
rs7942246	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7943416	1.00[ASN][1000 genomes]
rs7946524	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs923531	1.00[CHB][hapmap]
rs939106	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	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:84 , 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	chr11:46000800-46006200	Enhancers	Fetal Heart	heart
6	chr11:46000800-46010200	Weak transcription	Liver	Liver
7	chr11:46000800-46012400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr11:46001000-46015400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr11:46001400-46013200	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:46001400-46013600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr11:46001400-46015200	Weak transcription	Pancreas	Pancrea
12	chr11:46001400-46016000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr11:46001400-46070400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr11:46001600-46006800	Weak transcription	Thymus	Thymus
15	chr11:46001600-46007200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr11:46001600-46015200	Weak transcription	Fetal Muscle Trunk	muscle
17	chr11:46001600-46015400	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr11:46001600-46016400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:46001600-46021000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr11:46002000-46015000	Weak transcription	Fetal Muscle Leg	muscle
21	chr11:46002000-46025000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr11:46002000-46042400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr11:46002000-46056200	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr11:46002200-46024800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr11:46002200-46025000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr11:46002600-46012000	Weak transcription	GM12878-XiMat	blood
27	chr11:46002600-46023200	Weak transcription	Primary B cells from peripheral blood	blood
28	chr11:46003600-46006200	Enhancers	H1 Cell Line	embryonic stem cell
29	chr11:46003600-46006400	Enhancers	Fetal Brain Male	brain
30	chr11:46003600-46006800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr11:46003800-46006200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr11:46003800-46006400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr11:46004000-46006200	Enhancers	Brain Substantia Nigra	brain
34	chr11:46004000-46007000	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr11:46004000-46007600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:46004200-46006000	Enhancers	Brain Anterior Caudate	brain
37	chr11:46004200-46006000	Enhancers	Brain Inferior Temporal Lobe	brain
38	chr11:46004200-46006200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:46004400-46006000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr11:46004400-46006000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr11:46004400-46006000	Enhancers	H9 Cell Line	embryonic stem cell
42	chr11:46004400-46006000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:46004400-46006200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr11:46004600-46007800	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr11:46004600-46012400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr11:46004800-46006400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr11:46004800-46006800	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr11:46004800-46007800	Weak transcription	Gastric	stomach
49	chr11:46004800-46009200	Weak transcription	Fetal Kidney	kidney
50	chr11:46004800-46011200	Weak transcription	HUVEC	blood vessel

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links