Variant report

Variant	rs516041
Chromosome Location	chr11:64492069-64492070
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:64491342-64494192	HL-60	blood:	n/a	n/a
2	POLR2A	chr11:64491423-64494233	HL-60	blood:	n/a	n/a
3	RAD21	chr11:64490445-64492076	SK-N-SH	brain:	n/a	chr11:64490998-64491007 chr11:64491101-64491120 chr11:64490457-64490471 chr11:64491103-64491115 chr11:64491105-64491119
4	EP300	chr11:64490408-64492176	SK-N-SH	brain:	n/a	chr11:64490825-64490841 chr11:64490790-64490803
5	SMC3	chr11:64490407-64492108	SK-N-SH	brain:	n/a	chr11:64491105-64491119
6	CTCF	chr11:64492040-64492190	GM12878	blood:	n/a	chr11:64492167-64492176

No.	Distal block	Cell Line	Cell type
1	chr11:64489616..64492284-chr11:64509871..64511516,3	K562	blood:
2	chr11:64490193..64492198-chr11:64544563..64546459,2	MCF-7	breast:
3	chr11:64455433..64456290-chr11:64492003..64492618,2	MCF-7	breast:
4	chr11:64489234..64490973-chr11:64491983..64494707,2	K562	blood:
5	chr11:64478255..64481463-chr11:64489766..64492365,3	K562	blood:
6	chr11:64421324..64422093-chr11:64491806..64492706,2	K562	blood:
7	chr11:64490664..64492722-chr11:64991494..64993936,2	MCF-7	breast:
8	chr11:64491144..64492732-chr11:64505276..64507287,3	K562	blood:
9	chr11:64489351..64492621-chr11:64507509..64512935,5	K562	blood:

Variant related genes	Relation type
NRXN2	TF binding region
ENSG00000110076	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000068831	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10466694	1.00[EUR][1000 genomes]
rs11231806	1.00[EUR][1000 genomes]
rs11231811	1.00[EUR][1000 genomes]
rs11231812	1.00[EUR][1000 genomes]
rs11231865	1.00[EUR][1000 genomes]
rs11231866	1.00[EUR][1000 genomes]
rs11821081	1.00[EUR][1000 genomes]
rs1207182	0.81[AFR][1000 genomes]
rs1212539	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1212851	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12273948	1.00[EUR][1000 genomes]
rs12281931	1.00[EUR][1000 genomes]
rs12293573	1.00[EUR][1000 genomes]
rs17146100	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17146110	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1787671	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2022049	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2518908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2666561	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	0.82[AFR][1000 genomes];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[EUR][1000 genomes]
rs475704	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs512926	1.00[EUR][1000 genomes]
rs534052	1.00[AMR][1000 genomes]
rs534073	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs535606	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[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs546323	0.93[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs547280	0.96[YRI][hapmap]
rs550930	0.96[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs553618	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs559095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs559977	1.00[YRI][hapmap];0.97[AFR][1000 genomes];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	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[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]
rs7948607	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7948832	1.00[EUR][1000 genomes]
rs9326433	1.00[EUR][1000 genomes]
rs9326434	1.00[EUR][1000 genomes]
rs9666331	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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	nsv1049744	chr11:64486615-64630149	Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
21	nsv832189	chr11:64487183-64620199	Weak transcription Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
22	esv3324432	chr11:64489201-64492249	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs516041	SF1	cis	multi-tissue	Pritchard

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64490800-64492200	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr11:64490800-64498000	Enhancers	Liver	Liver
3	chr11:64491000-64494200	Enhancers	Fetal Brain Male	brain
4	chr11:64491000-64502200	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:64491200-64492200	Bivalent Enhancer	Fetal Intestine Large	intestine
6	chr11:64491200-64492400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr11:64491200-64492400	Weak transcription	Thymus	Thymus
8	chr11:64491200-64492600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr11:64491200-64492800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:64491200-64492800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr11:64491200-64493000	Enhancers	Primary hematopoietic stem cells	blood
12	chr11:64491200-64493000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr11:64491200-64493200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr11:64491200-64493600	Enhancers	Primary hematopoietic stem cells short term culture	blood
15	chr11:64491200-64493600	Enhancers	Fetal Thymus	thymus
16	chr11:64491200-64493800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr11:64491200-64494000	Enhancers	Primary T cells fromperipheralblood	blood
18	chr11:64491200-64494200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr11:64491200-64494200	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr11:64491200-64494200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
21	chr11:64491200-64494400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:64491200-64494800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr11:64491200-64496000	Weak transcription	Aorta	Aorta
24	chr11:64491200-64496200	Weak transcription	Lung	lung
25	chr11:64491200-64497600	Weak transcription	Right Ventricle	heart
26	chr11:64491200-64499200	Weak transcription	Left Ventricle	heart
27	chr11:64491200-64502200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr11:64491200-64502400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr11:64491200-64502800	Weak transcription	Gastric	stomach
30	chr11:64491400-64492200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
31	chr11:64491400-64492400	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr11:64491400-64492600	Enhancers	Brain Germinal Matrix	brain
33	chr11:64491400-64493000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr11:64491400-64493200	Enhancers	Primary B cells from peripheral blood	blood
35	chr11:64491400-64493200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr11:64491400-64493400	Enhancers	Primary B cells from cord blood	blood
37	chr11:64491400-64493600	Enhancers	Monocytes-CD14+_RO01746	blood
38	chr11:64491400-64493800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:64491400-64494200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr11:64491400-64494400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr11:64491400-64494600	Enhancers	H1 Cell Line	embryonic stem cell
42	chr11:64491400-64494800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr11:64491400-64494800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr11:64491400-64502200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr11:64491400-64503000	Weak transcription	Colon Smooth Muscle	Colon
46	chr11:64491400-64509400	Weak transcription	Right Atrium	heart
47	chr11:64491400-64509600	Weak transcription	Brain Angular Gyrus	brain
48	chr11:64491400-64509600	Weak transcription	Pancreas	Pancrea
49	chr11:64491600-64492400	Enhancers	Fetal Brain Female	brain
50	chr11:64491600-64492800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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