Variant report

Variant	rs55911307
Chromosome Location	chr2:55340725-55340726
allele	A/G
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	CEBPB	chr2:55340720-55340881	HepG2	liver:	n/a	chr2:55340800-55340811
2	RCOR1	chr2:55338384-55341644	IMR90	lung:	n/a	n/a
3	MAX	chr2:55338540-55340760	NB4	blood:	n/a	chr2:55339038-55339047
4	POLR2A	chr2:55338458-55341172	HL-60	blood:	n/a	n/a
5	CEBPB	chr2:55340664-55340864	HepG2	liver:	n/a	chr2:55340800-55340811

No.	Distal block	Cell Line	Cell type
1	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
2	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:
3	chr2:55339781..55342552-chr2:55346442..55349594,4	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs55664473	1.00[AMR][1000 genomes]
rs55700934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56039015	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56181361	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs56760831	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57385616	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59078210	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59657596	0.93[AFR][1000 genomes]
rs60068576	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72914557	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73936839	1.00[AFR][1000 genomes];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	nsv1006172	chr2:55322883-55340812	Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv999212	chr2:55324276-55340812	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1004503	chr2:55324276-55343705	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv997458	chr2:55324276-55344326	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1013316	chr2:55324276-55345262	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55329600-55342600	Weak transcription	NHEK	skin
2	chr2:55332000-55343400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:55334400-55340800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:55335400-55341000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
5	chr2:55337200-55341000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:55337200-55351000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr2:55337400-55342800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:55337400-55342800	Weak transcription	HMEC	breast
9	chr2:55338200-55341200	Enhancers	Duodenum Smooth Muscle	Duodenum
10	chr2:55338400-55340800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr2:55338400-55341000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:55338400-55341200	Enhancers	Stomach Mucosa	stomach
13	chr2:55338400-55343400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr2:55338400-55343400	Enhancers	Primary hematopoietic stem cells	blood
15	chr2:55338600-55340800	Flanking Active TSS	Brain Hippocampus Middle	brain
16	chr2:55338600-55340800	Enhancers	Duodenum Mucosa	Duodenum
17	chr2:55338600-55340800	Enhancers	Rectal Mucosa Donor 29	rectum
18	chr2:55338600-55340800	Enhancers	Right Atrium	heart
19	chr2:55338600-55341000	Enhancers	Cortex derived primary cultured neurospheres	brain
20	chr2:55338600-55341000	Enhancers	Placenta	Placenta
21	chr2:55338600-55341000	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr2:55338600-55341000	Enhancers	Right Ventricle	heart
23	chr2:55338600-55341200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr2:55338600-55341200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr2:55338600-55341400	Flanking Active TSS	HSMMtube	muscle
26	chr2:55338600-55341400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr2:55338600-55341600	Enhancers	Fetal Thymus	thymus
28	chr2:55338600-55343800	Enhancers	Fetal Muscle Leg	muscle
29	chr2:55338800-55340800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:55338800-55340800	Enhancers	Fetal Heart	heart
31	chr2:55338800-55341000	Enhancers	Fetal Lung	lung
32	chr2:55339000-55340800	Enhancers	Primary B cells from peripheral blood	blood
33	chr2:55339000-55340800	Enhancers	Spleen	Spleen
34	chr2:55339000-55341000	Enhancers	Psoas Muscle	Psoas
35	chr2:55339000-55341200	Enhancers	Primary B cells from cord blood	blood
36	chr2:55339200-55340800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
37	chr2:55339200-55340800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr2:55339200-55343000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:55339400-55351000	Weak transcription	H9 Cell Line	embryonic stem cell
40	chr2:55339600-55341400	Enhancers	NHDF-Ad	bronchial
41	chr2:55339600-55342200	Weak transcription	Hela-S3	cervix
42	chr2:55339600-55342600	Enhancers	A549	lung
43	chr2:55339600-55345800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr2:55339600-55345800	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr2:55339600-55345800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr2:55339600-55346800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:55339600-55347000	Weak transcription	Left Ventricle	heart
48	chr2:55339800-55340800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr2:55339800-55341000	Enhancers	Osteobl	bone
50	chr2:55339800-55341200	Enhancers	Colon Smooth Muscle	Colon

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