Variant report

Variant	rs555974
Chromosome Location	chr11:64516477-64516478
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:64514464..64517911-chr11:64519413..64523331,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000068976	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10897524	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11231859	0.88[EUR][1000 genomes]
rs1207113	0.91[ASN][1000 genomes]
rs1207181	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12223914	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1633462	0.83[EUR][1000 genomes]
rs2003293	0.88[EUR][1000 genomes]
rs2073797	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2073798	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230414	0.88[EUR][1000 genomes]
rs2267918	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2284301	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2375335	0.86[EUR][1000 genomes]
rs2959652	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3809076	0.83[EUR][1000 genomes]
rs474707	0.85[EUR][1000 genomes]
rs477549	0.86[EUR][1000 genomes]
rs483962	0.88[EUR][1000 genomes]
rs487105	0.83[EUR][1000 genomes]
rs489192	0.80[ASN][1000 genomes]
rs490980	0.83[EUR][1000 genomes]
rs494128	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs496914	0.90[EUR][1000 genomes]
rs523200	0.85[EUR][1000 genomes]
rs532747	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs547066	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs569602	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs580374	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58483071	0.88[EUR][1000 genomes]
rs589691	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs593394	0.83[EUR][1000 genomes]
rs620006	0.85[EUR][1000 genomes]
rs625172	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs630966	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs633923	0.85[EUR][1000 genomes]
rs637332	0.88[EUR][1000 genomes]
rs667237	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs673224	0.80[EUR][1000 genomes]
rs674297	0.81[EUR][1000 genomes]
rs680273	0.82[EUR][1000 genomes]
rs686171	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs693235	0.81[AMR][1000 genomes]
rs72643567	0.82[EUR][1000 genomes]
rs72643568	0.82[EUR][1000 genomes]
rs7938455	0.98[EUR][1000 genomes];0.86[ASN][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	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
16	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
17	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
18	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
19	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
20	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
21	nsv897701	chr11:64501991-64520569	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs555974	SF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64512800-64526400	Weak transcription	Ovary	ovary
2	chr11:64513400-64517600	Weak transcription	Colon Smooth Muscle	Colon
3	chr11:64513400-64529800	Weak transcription	Liver	Liver
4	chr11:64513400-64530000	Weak transcription	Aorta	Aorta
5	chr11:64513600-64518800	Weak transcription	Brain Substantia Nigra	brain
6	chr11:64513600-64518800	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr11:64513600-64518800	Weak transcription	Left Ventricle	heart
8	chr11:64513600-64522200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:64513600-64525600	Weak transcription	Psoas Muscle	Psoas
10	chr11:64513600-64526200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr11:64513600-64526200	Weak transcription	Esophagus	oesophagus
12	chr11:64513800-64517600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr11:64513800-64517800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:64513800-64519200	Weak transcription	Brain Anterior Caudate	brain
15	chr11:64513800-64526400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:64513800-64526800	Weak transcription	Brain Hippocampus Middle	brain
17	chr11:64513800-64526800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr11:64514000-64517600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr11:64514000-64518800	Weak transcription	Lung	lung
20	chr11:64514000-64518800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:64514000-64521000	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr11:64514000-64526800	Weak transcription	Brain Cingulate Gyrus	brain
23	chr11:64514000-64529800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr11:64514200-64517600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr11:64514200-64517600	Weak transcription	Fetal Stomach	stomach
26	chr11:64514200-64517800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr11:64514200-64517800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr11:64514200-64517800	Weak transcription	Adipose Nuclei	Adipose
29	chr11:64514200-64517800	Weak transcription	Thymus	Thymus
30	chr11:64514200-64518000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr11:64514200-64518000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr11:64514200-64518000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr11:64514200-64519000	Weak transcription	Gastric	stomach
34	chr11:64514200-64519200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr11:64514200-64522400	Weak transcription	Fetal Heart	heart
36	chr11:64514400-64517600	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr11:64514400-64517800	Weak transcription	Right Ventricle	heart
38	chr11:64514400-64518600	Weak transcription	Spleen	Spleen
39	chr11:64514400-64526600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr11:64514600-64517600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr11:64514600-64517800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr11:64514600-64529800	Weak transcription	Dnd41	blood
43	chr11:64514800-64516800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr11:64514800-64517600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
45	chr11:64514800-64517600	Weak transcription	Primary T cells from cord blood	blood
46	chr11:64514800-64517800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr11:64515000-64516800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
48	chr11:64515000-64517600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr11:64515000-64518000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr11:64515200-64517600	Weak transcription	Primary T helper cells fromperipheralblood	blood

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