Variant report

Variant	rs580374
Chromosome Location	chr11:64499482-64499483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	11:64499245-64501239..11:64523887-64530985	Hela-S3	cervix:
2	11:64207610-64216678..11:64499245-64501239	Hela-S3	cervix:
3	chr11:64476395..64479259-chr11:64497435..64499658,2	K562	blood:
4	chr11:64498850..64501502-chr11:64505614..64507569,2	K562	blood:
5	chr11:64496720..64499587-chr11:64508589..64511538,2	K562	blood:
6	11:64402707-64415880..11:64499245-64501239	Hela-S3	cervix:
7	chr11:64496428..64500797-chr11:64501095..64504421,5	K562	blood:
8	11:64415880-64426617..11:64499245-64501239	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000181908	Chromatin interaction
ENSG00000068976	Chromatin interaction
ENSG00000237410	Chromatin interaction
ENSG00000068831	Chromatin interaction
ENSG00000110076	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10400348	0.85[EUR][1000 genomes]
rs10792444	0.87[EUR][1000 genomes]
rs10897524	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11231853	0.87[EUR][1000 genomes]
rs11231859	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1207113	0.85[ASN][1000 genomes]
rs1207181	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12223914	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12417551	0.88[EUR][1000 genomes]
rs12575704	0.87[EUR][1000 genomes]
rs1633462	0.93[EUR][1000 genomes]
rs17146121	0.84[EUR][1000 genomes]
rs2003293	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2073797	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2073798	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2230414	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2267918	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2284301	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2375335	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2959652	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3741398	0.87[EUR][1000 genomes]
rs3809076	0.93[EUR][1000 genomes]
rs474707	0.95[EUR][1000 genomes]
rs476037	0.83[EUR][1000 genomes]
rs477549	0.97[EUR][1000 genomes]
rs483962	0.98[EUR][1000 genomes]
rs487105	0.93[EUR][1000 genomes]
rs489192	0.84[EUR][1000 genomes]
rs490980	0.90[EUR][1000 genomes]
rs494128	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs496914	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs523200	0.95[EUR][1000 genomes]
rs523752	0.83[EUR][1000 genomes]
rs532747	0.88[EUR][1000 genomes]
rs547066	0.86[EUR][1000 genomes]
rs555974	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs569602	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58483071	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs589691	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs593394	0.93[EUR][1000 genomes]
rs606458	0.89[EUR][1000 genomes]
rs607389	0.86[EUR][1000 genomes]
rs620006	0.95[EUR][1000 genomes]
rs625172	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs630966	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs633923	0.95[EUR][1000 genomes]
rs637332	0.98[EUR][1000 genomes]
rs667237	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs674297	0.91[EUR][1000 genomes]
rs680273	0.92[EUR][1000 genomes]
rs683841	0.84[EUR][1000 genomes]
rs684720	0.84[EUR][1000 genomes]
rs686171	0.86[EUR][1000 genomes]
rs693235	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs72643567	0.92[EUR][1000 genomes]
rs72643568	0.92[EUR][1000 genomes]
rs7938455	0.88[EUR][1000 genomes]
rs7939965	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs580374	SF1	Cis_1M	lymphoblastoid	RTeQTL
rs580374	SF1	cis	multi-tissue	Pritchard

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64491000-64502200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr11:64491200-64502200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr11:64491200-64502400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr11:64491200-64502800	Weak transcription	Gastric	stomach
5	chr11:64491400-64502200	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr11:64491400-64503000	Weak transcription	Colon Smooth Muscle	Colon
7	chr11:64491400-64509400	Weak transcription	Right Atrium	heart
8	chr11:64491400-64509600	Weak transcription	Brain Angular Gyrus	brain
9	chr11:64491400-64509600	Weak transcription	Pancreas	Pancrea
10	chr11:64491600-64502600	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr11:64491600-64503200	Weak transcription	Esophagus	oesophagus
12	chr11:64491600-64509200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr11:64491600-64509400	Weak transcription	Brain Hippocampus Middle	brain
14	chr11:64491800-64509400	Weak transcription	Brain Substantia Nigra	brain
15	chr11:64491800-64509800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr11:64492000-64509600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr11:64493400-64502200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:64493400-64508800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr11:64493600-64499800	Strong transcription	Stomach Smooth Muscle	stomach
20	chr11:64493600-64502600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr11:64493600-64503800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr11:64493600-64507800	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr11:64493600-64508000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr11:64493800-64500000	Strong transcription	Primary B cells from cord blood	blood
25	chr11:64493800-64500800	Strong transcription	Primary T helper cells fromperipheralblood	blood
26	chr11:64493800-64503600	Strong transcription	Primary B cells from peripheral blood	blood
27	chr11:64494000-64508400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr11:64494000-64508600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr11:64494000-64508600	Strong transcription	Primary T cells from cord blood	blood
30	chr11:64494000-64508600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:64494200-64501000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr11:64494200-64501400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr11:64494200-64503400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr11:64494600-64499800	Strong transcription	Primary hematopoietic stem cells	blood
35	chr11:64494800-64503200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr11:64495200-64499600	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr11:64495200-64499800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr11:64495600-64499800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr11:64495600-64499800	Strong transcription	Thymus	Thymus
40	chr11:64495800-64505200	Strong transcription	Fetal Thymus	thymus
41	chr11:64496600-64502200	Weak transcription	Lung	lung
42	chr11:64496600-64502400	Weak transcription	Aorta	Aorta
43	chr11:64497200-64499800	Enhancers	Brain Germinal Matrix	brain
44	chr11:64497600-64499600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:64497800-64499800	Enhancers	Fetal Brain Female	brain
46	chr11:64497800-64499800	Strong transcription	Dnd41	blood
47	chr11:64497800-64500000	Strong transcription	Primary T killer memory cells from peripheral blood	blood
48	chr11:64497800-64504000	Weak transcription	Placenta	Placenta
49	chr11:64498000-64499600	Enhancers	iPS-18 Cell Line	embryonic stem cell
50	chr11:64498000-64502200	Weak transcription	Liver	Liver

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