Variant report

Variant	rs2666561
Chromosome Location	chr11:64479757-64479758
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	chr11:64478005..64481824-chr11:64534394..64538447,4	K562	blood:
2	chr11:64478255..64481463-chr11:64489766..64492365,3	K562	blood:

Variant related genes	Relation type
ENSG00000110076	Chromatin interaction
ENSG00000168066	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10466694	1.00[EUR][1000 genomes]
rs11231806	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11231811	1.00[EUR][1000 genomes]
rs11231812	1.00[EUR][1000 genomes]
rs11231865	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs11231866	1.00[EUR][1000 genomes]
rs11231892	1.00[MEX][hapmap]
rs11821081	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1212539	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1212851	1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12273948	1.00[EUR][1000 genomes]
rs12280878	1.00[TSI][hapmap]
rs12281931	1.00[EUR][1000 genomes]
rs12293573	1.00[EUR][1000 genomes]
rs12294207	1.00[MEX][hapmap]
rs17146100	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17146110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17146119	1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap]
rs17159320	1.00[MEX][hapmap]
rs17159321	1.00[MEX][hapmap]
rs1787671	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2022048	1.00[TSI][hapmap]
rs2022049	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2518908	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2666562	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2904961	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2959651	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3016758	1.00[EUR][1000 genomes]
rs3016759	1.00[AMR][1000 genomes]
rs41323046	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs475704	1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs512926	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs516041	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs534052	1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]
rs534073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs535606	1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs541305	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs545167	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs545819	1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs546323	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs547280	0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap]
rs550930	0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs553618	0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs559095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs559977	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56186064	1.00[EUR][1000 genomes]
rs565688	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs573545	0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs579175	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58571986	1.00[EUR][1000 genomes]
rs6591863	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs7110778	1.00[EUR][1000 genomes]
rs7113097	1.00[EUR][1000 genomes]
rs7127435	1.00[EUR][1000 genomes]
rs73492134	1.00[AMR][1000 genomes]
rs73492139	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73492140	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73492144	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73494206	1.00[EUR][1000 genomes]
rs7927181	1.00[TSI][hapmap]
rs7948607	1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7948832	1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9326433	1.00[EUR][1000 genomes]
rs9326434	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs9666331	1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2422214	chr11:64312491-64483418	Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv832188	chr11:64315368-64485209	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv468596	chr11:64334114-64527080	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
4	nsv555195	chr11:64334114-64527080	Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv897694	chr11:64334114-64584959	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
6	nsv818842	chr11:64345448-64546391	Bivalent Enhancer Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
7	nsv528506	chr11:64345448-64701030	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
8	nsv555196	chr11:64357072-64559898	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
9	nsv897695	chr11:64357072-64701030	Weak transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1075 gene(s)	inside rSNPs	diseases
10	nsv1051350	chr11:64372906-64533632	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
11	nsv555198	chr11:64373899-64573589	Weak transcription Transcr. at gene 5' and 3' Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
12	esv1804443	chr11:64386453-64534785	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
13	nsv897697	chr11:64447420-64584959	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
14	nsv897698	chr11:64447420-64621573	Active TSS Bivalent Enhancer Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
15	nsv897699	chr11:64447420-64638041	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
16	nsv897700	chr11:64447420-64701030	Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1071 gene(s)	inside rSNPs	diseases
17	nsv359	chr11:64477008-64502873	Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
18	nsv555202	chr11:64477050-64573589	Strong transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
19	nsv468597	chr11:64477050-64584959	Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
20	nsv468598	chr11:64477050-64584959	Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
21	nsv555203	chr11:64477050-64584959	Strong transcription Genic enhancers Bivalent Enhancer Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
22	esv3436229	chr11:64478776-64483074	Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2666561	SF1	cis	lymphoblastoid	seeQTL

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64477800-64479800	Enhancers	Brain Substantia Nigra	brain
2	chr11:64477800-64479800	Flanking Active TSS	Fetal Brain Female	brain
3	chr11:64477800-64481600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr11:64478000-64480000	Enhancers	Brain Anterior Caudate	brain
5	chr11:64478000-64480200	Bivalent Enhancer	Fetal Muscle Leg	muscle
6	chr11:64478000-64480800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr11:64478000-64480800	Weak transcription	Right Atrium	heart
8	chr11:64478000-64481000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr11:64478200-64480200	Bivalent Enhancer	Brain Dorsolateral Prefrontal Cortex	brain
10	chr11:64478200-64480200	Bivalent Enhancer	Fetal Stomach	stomach
11	chr11:64478200-64480400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
12	chr11:64478200-64481000	Enhancers	Gastric	stomach
13	chr11:64478400-64479800	Bivalent Enhancer	Fetal Heart	heart
14	chr11:64478400-64480200	Bivalent Enhancer	Primary B cells from cord blood	blood
15	chr11:64478400-64480400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr11:64478400-64480400	Bivalent Enhancer	Fetal Brain Male	brain
17	chr11:64478400-64480600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
18	chr11:64478400-64480600	Bivalent Enhancer	Spleen	Spleen
19	chr11:64478600-64480200	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
20	chr11:64478600-64480200	Enhancers	Lung	lung
21	chr11:64478600-64480800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
22	chr11:64478600-64481600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
23	chr11:64478800-64480000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr11:64478800-64481600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
25	chr11:64478800-64481600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr11:64479000-64479800	Flanking Bivalent TSS/Enh	ES-WA7 Cell Line	embryonic stem cell
27	chr11:64479000-64480200	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
28	chr11:64479000-64480600	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr11:64479000-64480800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
30	chr11:64479000-64481000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr11:64479200-64479800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
32	chr11:64479200-64480000	Bivalent Enhancer	Brain Hippocampus Middle	brain
33	chr11:64479200-64480200	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr11:64479200-64480600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
35	chr11:64479200-64480600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
36	chr11:64479400-64480000	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
37	chr11:64479400-64480200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
38	chr11:64479400-64480400	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:64479400-64480400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr11:64479400-64481000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
41	chr11:64479400-64481000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr11:64479600-64479800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr11:64479600-64479800	Bivalent Enhancer	Brain Germinal Matrix	brain
44	chr11:64479600-64479800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
45	chr11:64479600-64479800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
46	chr11:64479600-64480000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
47	chr11:64479600-64480000	Flanking Active TSS	K562	blood
48	chr11:64479600-64480200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
49	chr11:64479600-64480200	Bivalent Enhancer	Placenta	Placenta
50	chr11:64479600-64480400	Weak transcription	Pancreas	Pancrea

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