Variant report

Variant	rs55993793
Chromosome Location	chr2:55241711-55241712
allele	A/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	FOS	chr2:55241650-55241826	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55240957..55243233-chr2:55273939..55276356,2	K562	blood:
2	chr2:55241176..55242945-chr2:55276344..55278140,2	MCF-7	breast:
3	chr2:55236989..55239116-chr2:55240470..55242602,2	K562	blood:
4	chr2:55241702..55243264-chr2:55276241..55278692,2	MCF-7	breast:

Variant related genes	Relation type
RTN4	TF binding region
RNU6-433P	TF binding region
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10170340	0.90[ASN][1000 genomes]
rs12464447	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12469804	0.82[ASN][1000 genomes]
rs12475787	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12475904	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17046570	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17046594	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17347089	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17418675	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2289747	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2864049	0.91[ASN][1000 genomes]
rs55659423	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55698303	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55762835	0.80[ASN][1000 genomes]
rs56013263	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6707036	0.81[EUR][1000 genomes]
rs67156582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72795431	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72795440	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7582359	0.81[EUR][1000 genomes]
rs7601625	0.82[ASN][1000 genomes]
rs887	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55232200-55244800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:55234800-55244800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:55234800-55246000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:55236800-55243400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr2:55237000-55243600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr2:55237400-55242800	Enhancers	HSMMtube	muscle
8	chr2:55237600-55242000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:55237600-55243600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:55237600-55246000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:55237600-55247800	Weak transcription	Left Ventricle	heart
12	chr2:55237600-55249600	Weak transcription	Gastric	stomach
13	chr2:55237600-55250200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:55237600-55258600	Weak transcription	Ovary	ovary
15	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
16	chr2:55237800-55242200	Enhancers	NHLF	lung
17	chr2:55237800-55242800	Enhancers	Brain Substantia Nigra	brain
18	chr2:55237800-55242800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:55237800-55242800	Enhancers	Rectal Smooth Muscle	rectum
20	chr2:55237800-55243000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr2:55237800-55243400	Enhancers	Osteobl	bone
22	chr2:55237800-55243600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:55237800-55243600	Enhancers	Brain Hippocampus Middle	brain
24	chr2:55238000-55243000	Enhancers	Adipose Nuclei	Adipose
25	chr2:55238200-55245800	Weak transcription	Brain Germinal Matrix	brain
26	chr2:55238400-55242400	Enhancers	Liver	Liver
27	chr2:55238400-55242600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:55238400-55244600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:55238400-55249200	Weak transcription	Pancreas	Pancrea
30	chr2:55238400-55249600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:55238400-55250800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr2:55238400-55251200	Weak transcription	Psoas Muscle	Psoas
33	chr2:55238400-55252200	Weak transcription	Fetal Thymus	thymus
34	chr2:55238400-55252400	Weak transcription	Thymus	Thymus
35	chr2:55238400-55253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:55239000-55241800	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr2:55239200-55243000	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr2:55239200-55244600	Weak transcription	Primary B cells from cord blood	blood
39	chr2:55239200-55244800	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:55239200-55247800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:55239400-55242400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:55239400-55243200	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr2:55239400-55243400	Genic enhancers	HSMM	muscle
44	chr2:55239400-55244800	Enhancers	Muscle Satellite Cultured Cells	--
45	chr2:55239400-55245000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr2:55239600-55241800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:55239600-55242200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr2:55239600-55242400	Enhancers	HepG2	liver
49	chr2:55239600-55243600	Weak transcription	Aorta	Aorta
50	chr2:55239800-55242000	Enhancers	Brain Anterior Caudate	brain

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