Variant report

Variant	rs669976
Chromosome Location	chr11:64573589-64573590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64569062..64575536-chr11:64608720..64614805,15	MCF-7	breast:
2	chr11:64571014..64575800-chr11:64609684..64614421,7	K562	blood:
3	chr11:64568489..64574764-chr11:64609155..64613913,19	MCF-7	breast:
4	chr11:64567558..64572906-chr11:64572928..64575629,5	MCF-7	breast:
5	chr11:64509857..64513722-chr11:64571129..64574033,3	MCF-7	breast:
6	chr11:64543661..64548104-chr11:64572931..64579605,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068831	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000171219	Chromatin interaction
ENSG00000269038	Chromatin interaction
ENSG00000168067	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10897525	0.88[MEX][hapmap]
rs11231859	0.90[CEU][hapmap];0.83[MEX][hapmap]
rs11231869	0.88[MEX][hapmap]
rs1143937	0.90[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1633462	0.89[CEU][hapmap]
rs17146121	0.80[CEU][hapmap];0.88[MEX][hapmap]
rs2267918	0.90[CEU][hapmap];0.83[MEX][hapmap]
rs2284301	0.90[CEU][hapmap];0.83[MEX][hapmap]
rs2959652	0.90[CEU][hapmap]
rs3741398	0.90[CEU][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap]
rs3809076	0.80[CEU][hapmap];0.88[MEX][hapmap]
rs474707	0.86[GIH][hapmap];0.89[MEX][hapmap]
rs477549	0.90[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap]
rs483962	0.90[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap]
rs487105	0.90[CEU][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap]
rs489192	0.90[CEU][hapmap]
rs496914	0.90[CEU][hapmap]
rs509606	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs523200	0.90[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap]
rs532747	0.88[MEX][hapmap]
rs547066	0.87[MEX][hapmap]
rs559566	0.81[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs569602	0.88[MEX][hapmap]
rs589691	0.90[CEU][hapmap]
rs600347	0.92[ASN][1000 genomes]
rs606458	0.90[CEU][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap]
rs607389	0.90[CEU][hapmap]
rs624975	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs637332	0.90[CEU][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap]
rs677298	0.90[CEU][hapmap];0.85[CHB][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.94[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes]
rs67808744	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs680273	0.90[CEU][hapmap];0.84[MEX][hapmap]
rs693235	0.81[CEU][hapmap]
rs7939965	0.80[CEU][hapmap];0.88[MEX][hapmap]

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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	nsv469962	chr11:64527080-64621573	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
16	nsv897702	chr11:64532579-64584231	Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
17	nsv897703	chr11:64538346-64574200	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
18	nsv519117	chr11:64546391-64573589	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
19	nsv519478	chr11:64546391-64584987	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
20	nsv555204	chr11:64561200-64574200	Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
21	nsv555205	chr11:64561200-64575505	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
22	nsv555206	chr11:64563757-64574200	Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs669976	SF1	Cis_1M	lymphoblastoid	RTeQTL
rs669976	SF1	cis	multi-tissue	Pritchard

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64571400-64577000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:64571600-64574400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr11:64571600-64576600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr11:64571800-64573600	Genic enhancers	Stomach Smooth Muscle	stomach
5	chr11:64571800-64574400	Genic enhancers	Spleen	Spleen
6	chr11:64571800-64575000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr11:64571800-64575200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr11:64571800-64575600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr11:64571800-64575800	Strong transcription	Thymus	Thymus
10	chr11:64571800-64576200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:64571800-64576600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:64571800-64576600	Weak transcription	GM12878-XiMat	blood
13	chr11:64571800-64576800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr11:64571800-64576800	Weak transcription	Psoas Muscle	Psoas
15	chr11:64571800-64576800	Weak transcription	HUVEC	blood vessel
16	chr11:64571800-64576800	Weak transcription	NH-A	brain
17	chr11:64571800-64577000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr11:64571800-64577000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr11:64571800-64577000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr11:64571800-64577000	Weak transcription	HSMMtube	muscle
21	chr11:64572000-64573600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr11:64572000-64573800	Weak transcription	HepG2	liver
23	chr11:64572000-64574400	Weak transcription	NHDF-Ad	bronchial
24	chr11:64572000-64575000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr11:64572000-64575000	Strong transcription	Brain Germinal Matrix	brain
26	chr11:64572000-64575000	Strong transcription	Duodenum Mucosa	Duodenum
27	chr11:64572000-64575200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr11:64572000-64575200	Strong transcription	Fetal Brain Female	brain
29	chr11:64572000-64575200	Weak transcription	Fetal Kidney	kidney
30	chr11:64572000-64575200	Strong transcription	Lung	lung
31	chr11:64572000-64575400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr11:64572000-64575400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr11:64572000-64575400	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr11:64572000-64575600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr11:64572000-64575600	Strong transcription	Brain Anterior Caudate	brain
36	chr11:64572000-64575600	Strong transcription	Brain Hippocampus Middle	brain
37	chr11:64572000-64575600	Strong transcription	Skeletal Muscle Female	skeletal muscle
38	chr11:64572000-64575600	Strong transcription	Osteobl	bone
39	chr11:64572000-64575800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr11:64572000-64575800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr11:64572000-64575800	Strong transcription	Primary T cells from cord blood	blood
42	chr11:64572000-64576000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr11:64572000-64576000	Strong transcription	Brain Cingulate Gyrus	brain
44	chr11:64572000-64576000	Strong transcription	Fetal Lung	lung
45	chr11:64572000-64576000	Strong transcription	Fetal Thymus	thymus
46	chr11:64572000-64576000	Strong transcription	NHEK	skin
47	chr11:64572000-64576200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:64572000-64576200	Strong transcription	Brain Inferior Temporal Lobe	brain
49	chr11:64572000-64576400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr11:64572000-64576400	Strong transcription	Fetal Stomach	stomach

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