Variant report

Variant	rs56838978
Chromosome Location	chr11:85360514-85360515
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85337127..85343160-chr11:85357064..85364111,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171204	Chromatin interaction
ENSG00000150672	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10501593	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12099145	0.85[AMR][1000 genomes]
rs17148234	0.85[AMR][1000 genomes]
rs17148242	0.85[AMR][1000 genomes]
rs17148285	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs17148316	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs56047795	0.85[AMR][1000 genomes]
rs56401259	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs57309067	0.85[AMR][1000 genomes]
rs57313830	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57361884	0.85[AMR][1000 genomes]
rs60032790	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs60192818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60734322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60865542	0.82[AFR][1000 genomes]
rs61169921	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs61180955	0.85[AMR][1000 genomes]
rs61198962	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61465434	0.85[AMR][1000 genomes]
rs6592254	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6592256	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6592257	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7116532	0.85[AMR][1000 genomes]
rs7116553	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7122987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs744173	1.00[AMR][1000 genomes]
rs7938991	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7942218	0.85[AMR][1000 genomes]
rs7946793	0.90[AFR][1000 genomes]
rs7949114	1.00[AMR][1000 genomes]
rs7952219	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv898047	chr11:85180409-85377707	Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
6	nsv898048	chr11:85206156-85404138	Flanking Active TSS Genic enhancers Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh 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	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85359400-85360600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
2	chr11:85359400-85360800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr11:85359400-85360800	Flanking Active TSS	Dnd41	blood
4	chr11:85359400-85362200	Weak transcription	Spleen	Spleen
5	chr11:85359400-85370400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:85359400-85373000	Weak transcription	Small Intestine	intestine
7	chr11:85359400-85374000	Weak transcription	Esophagus	oesophagus
8	chr11:85359600-85360800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:85359600-85360800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr11:85359600-85362200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr11:85359600-85362200	Weak transcription	Left Ventricle	heart
12	chr11:85359600-85373000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:85359600-85373400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr11:85359800-85360600	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr11:85359800-85360600	Enhancers	Fetal Heart	heart
16	chr11:85359800-85360800	Enhancers	Muscle Satellite Cultured Cells	--
17	chr11:85359800-85360800	Enhancers	Brain Anterior Caudate	brain
18	chr11:85359800-85360800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr11:85359800-85360800	Enhancers	Fetal Brain Female	brain
20	chr11:85359800-85360800	Enhancers	Fetal Lung	lung
21	chr11:85359800-85360800	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr11:85359800-85360800	Enhancers	Stomach Mucosa	stomach
23	chr11:85359800-85361000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr11:85359800-85361000	Enhancers	Colon Smooth Muscle	Colon
25	chr11:85359800-85361400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr11:85359800-85361600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr11:85359800-85362000	Weak transcription	Fetal Kidney	kidney
28	chr11:85359800-85362200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:85359800-85362200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr11:85359800-85362200	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr11:85359800-85362200	Weak transcription	Primary B cells from cord blood	blood
32	chr11:85359800-85362200	Weak transcription	Rectal Smooth Muscle	rectum
33	chr11:85359800-85362800	Weak transcription	Aorta	Aorta
34	chr11:85359800-85362800	Weak transcription	Psoas Muscle	Psoas
35	chr11:85359800-85364000	Weak transcription	Placenta	Placenta
36	chr11:85359800-85364600	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr11:85359800-85364600	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr11:85359800-85364800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr11:85359800-85365000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr11:85359800-85366600	Weak transcription	HSMMtube	muscle
41	chr11:85359800-85366800	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr11:85359800-85368200	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr11:85359800-85372600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr11:85359800-85373000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr11:85359800-85373000	Weak transcription	H9 Cell Line	embryonic stem cell
46	chr11:85359800-85373000	Weak transcription	Ovary	ovary
47	chr11:85359800-85373200	Weak transcription	Fetal Stomach	stomach
48	chr11:85360000-85360600	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr11:85360000-85360600	Enhancers	Breast Myoepithelial Primary Cells	Breast
50	chr11:85360000-85360600	Enhancers	Primary T helper cells PMA-I stimulated	--

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