Variant report

Variant	rs56123312
Chromosome Location	chr2:54558233-54558234
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54341443..54343043-chr2:54557751..54559883,2	MCF-7	breast:
2	chr2:54341307..54344135-chr2:54557168..54559182,2	K562	blood:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs55830733	0.92[AFR][1000 genomes]
rs56324377	0.92[AFR][1000 genomes]
rs56368008	0.92[AFR][1000 genomes]
rs56764163	0.91[AFR][1000 genomes]
rs59891328	0.91[AFR][1000 genomes]
rs6710272	0.92[AFR][1000 genomes]
rs73931746	0.92[AFR][1000 genomes]
rs73933610	0.84[AFR][1000 genomes]
rs73933627	0.92[AFR][1000 genomes]
rs73933632	0.92[AFR][1000 genomes]
rs73933633	0.92[AFR][1000 genomes]
rs73933634	0.92[AFR][1000 genomes]
rs7592398	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv532512	chr2:54453210-54630755	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1004632	chr2:54469283-54590480	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54556800-54558400	Active TSS	Brain Substantia Nigra	brain
2	chr2:54556800-54558600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
3	chr2:54557000-54558400	Active TSS	H1 Cell Line	embryonic stem cell
4	chr2:54557000-54558400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr2:54557000-54558400	Active TSS	Aorta	Aorta
6	chr2:54557000-54558400	Active TSS	Right Ventricle	heart
7	chr2:54557000-54558600	Flanking Active TSS	Liver	Liver
8	chr2:54557000-54558800	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr2:54557000-54558800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr2:54557000-54558800	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr2:54557000-54558800	Flanking Active TSS	Dnd41	blood
12	chr2:54557200-54558400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr2:54557200-54558400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr2:54557200-54558400	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr2:54557200-54558400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr2:54557200-54558400	Active TSS	Left Ventricle	heart
17	chr2:54557200-54558400	Active TSS	Lung	lung
18	chr2:54557200-54558400	Active TSS	Ovary	ovary
19	chr2:54557200-54558400	Active TSS	Pancreas	Pancrea
20	chr2:54557200-54558400	Active TSS	Psoas Muscle	Psoas
21	chr2:54557200-54558400	Active TSS	NHDF-Ad	bronchial
22	chr2:54557200-54558600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
23	chr2:54557200-54558600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr2:54557200-54558600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:54557200-54558600	Active TSS	Brain Anterior Caudate	brain
26	chr2:54557200-54558600	Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr2:54557200-54558600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
28	chr2:54557200-54558600	Flanking Active TSS	HMEC	breast
29	chr2:54557200-54558600	Flanking Active TSS	HUVEC	blood vessel
30	chr2:54557200-54558800	Active TSS	Fetal Kidney	kidney
31	chr2:54557200-54558800	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr2:54557400-54558400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:54557400-54558400	Active TSS	HUES6 Cell Line	embryonic stem cell
34	chr2:54557400-54558400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr2:54557400-54558400	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr2:54557400-54558400	Flanking Active TSS	Primary B cells from peripheral blood	blood
37	chr2:54557400-54558400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
38	chr2:54557400-54558400	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr2:54557400-54558400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr2:54557400-54558400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
41	chr2:54557400-54558400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
42	chr2:54557400-54558400	Active TSS	Brain Angular Gyrus	brain
43	chr2:54557400-54558400	Active TSS	Brain Hippocampus Middle	brain
44	chr2:54557400-54558400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr2:54557400-54558400	Flanking Active TSS	Fetal Thymus	thymus
46	chr2:54557400-54558400	Active TSS	Rectal Smooth Muscle	rectum
47	chr2:54557400-54558600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr2:54557400-54558600	Active TSS	HSMM	muscle
49	chr2:54557400-54558800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:54557400-54558800	Active TSS	Fetal Brain Female	brain

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