Variant report

Variant	rs56004091
Chromosome Location	chr11:9862234-9862235
allele	C/T
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	FOXA1	chr11:9862066-9862336	T-47D	breast:	n/a	n/a
2	STAT3	chr11:9862170-9862503	MCF10A-Er-Src	breast:	n/a	chr11:9862322-9862333 chr11:9862328-9862335 chr11:9862324-9862333 chr11:9862323-9862332 chr11:9862321-9862335
3	RELA	chr11:9862174-9862511	GM12878	blood:	n/a	chr11:9862363-9862372 chr11:9862363-9862372
4	EP300	chr11:9862011-9862405	T-47D	breast:	n/a	n/a
5	STAT3	chr11:9862178-9862508	MCF10A-Er-Src	breast:	n/a	chr11:9862322-9862333 chr11:9862328-9862335 chr11:9862324-9862333 chr11:9862323-9862332 chr11:9862321-9862335
6	STAT3	chr11:9862150-9862508	MCF10A-Er-Src	breast:	n/a	chr11:9862322-9862333 chr11:9862328-9862335 chr11:9862324-9862333 chr11:9862323-9862332 chr11:9862321-9862335
7	TCF7L2	chr11:9862045-9862426	PANC-1	pancreas:	n/a	n/a

Variant related genes	Relation type
SBF2	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11821145	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11822070	1.00[AMR][1000 genomes]
rs11823024	1.00[AMR][1000 genomes]
rs11823620	1.00[AMR][1000 genomes]
rs11824133	1.00[AMR][1000 genomes]
rs11824944	1.00[AMR][1000 genomes]
rs11826573	1.00[AMR][1000 genomes]
rs55805230	1.00[AMR][1000 genomes]
rs57233768	1.00[AMR][1000 genomes]
rs57297566	1.00[AMR][1000 genomes]
rs57735272	1.00[AMR][1000 genomes]
rs57948595	1.00[AMR][1000 genomes]
rs58024914	1.00[AMR][1000 genomes]
rs58717942	1.00[AMR][1000 genomes]
rs58982478	1.00[AMR][1000 genomes]
rs73402415	1.00[AMR][1000 genomes]
rs73406739	1.00[AMR][1000 genomes]
rs73412193	1.00[AMR][1000 genomes]
rs73412196	1.00[AMR][1000 genomes]
rs73414129	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73416199	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73418575	1.00[AMR][1000 genomes]
rs73418583	1.00[AMR][1000 genomes]
rs73418601	1.00[AMR][1000 genomes]
rs73420636	1.00[AMR][1000 genomes]
rs73420638	1.00[AMR][1000 genomes]
rs73420639	1.00[AMR][1000 genomes]
rs73420640	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv896987	chr11:9759918-9885849	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	esv3384280	chr11:9766350-9911228	Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9818600-9881400	Weak transcription	Spleen	Spleen
2	chr11:9824200-9867600	Weak transcription	Psoas Muscle	Psoas
3	chr11:9826800-9868200	Weak transcription	Aorta	Aorta
4	chr11:9829600-9865600	Weak transcription	Gastric	stomach
5	chr11:9830000-9864400	Weak transcription	Esophagus	oesophagus
6	chr11:9830200-9863000	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr11:9830400-9880400	Weak transcription	Thymus	Thymus
8	chr11:9830800-9865600	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr11:9830800-9866800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr11:9830800-9880600	Weak transcription	Fetal Brain Male	brain
11	chr11:9833400-9868400	Weak transcription	Fetal Kidney	kidney
12	chr11:9833600-9878800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:9834200-9876600	Weak transcription	Brain Germinal Matrix	brain
14	chr11:9834600-9867400	Weak transcription	Brain Hippocampus Middle	brain
15	chr11:9834600-9877200	Weak transcription	Right Ventricle	heart
16	chr11:9837600-9863200	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr11:9837600-9885800	Weak transcription	Hela-S3	cervix
18	chr11:9838600-9879800	Weak transcription	Fetal Thymus	thymus
19	chr11:9848200-9877000	Weak transcription	HepG2	liver
20	chr11:9849000-9863000	Weak transcription	Ovary	ovary
21	chr11:9851200-9880000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr11:9851600-9875400	Weak transcription	Stomach Mucosa	stomach
23	chr11:9851600-9880400	Weak transcription	Small Intestine	intestine
24	chr11:9853000-9871600	Weak transcription	Fetal Intestine Small	intestine
25	chr11:9853400-9877400	Weak transcription	Brain Substantia Nigra	brain
26	chr11:9854000-9865600	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr11:9854000-9868400	Weak transcription	Lung	lung
28	chr11:9854000-9877400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr11:9854000-9880600	Weak transcription	Colonic Mucosa	Colon
30	chr11:9856600-9880000	Weak transcription	Fetal Heart	heart
31	chr11:9856800-9865600	Weak transcription	Pancreas	Pancrea
32	chr11:9859000-9872800	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr11:9859600-9862800	Enhancers	HSMM	muscle
34	chr11:9859600-9871400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr11:9859800-9863800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr11:9859800-9880200	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr11:9860600-9864200	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr11:9860600-9865600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:9860600-9867200	Weak transcription	NHLF	lung
40	chr11:9860800-9864200	Enhancers	Primary T cells from cord blood	blood
41	chr11:9860800-9864800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr11:9861000-9863400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr11:9861000-9863600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
44	chr11:9861000-9864000	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr11:9861000-9866800	Weak transcription	NH-A	brain
46	chr11:9861000-9868400	Weak transcription	Brain Angular Gyrus	brain
47	chr11:9861200-9862600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:9861200-9863000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr11:9861200-9863200	Weak transcription	Left Ventricle	heart
50	chr11:9861200-9863800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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