Variant report

Variant	rs11677099
Chromosome Location	chr2:55254165-55254166
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55253687..55256302-chr2:55275288..55279077,3	K562	blood:
2	chr2:55243166..55246645-chr2:55249862..55254918,6	K562	blood:
3	chr2:55251702..55254676-chr2:55343936..55346646,2	K562	blood:
4	chr2:55241211..55243006-chr2:55251751..55254579,2	K562	blood:
5	chr2:55252582..55260799-chr2:55274165..55279100,17	MCF-7	breast:
6	chr2:55253309..55255989-chr2:55259127..55262322,3	MCF-7	breast:
7	chr2:55251918..55254652-chr2:55395890..55398049,2	K562	blood:
8	chr2:55253656..55256107-chr2:55260589..55262893,2	K562	blood:
9	chr2:55253484..55256107-chr2:55261121..55262893,2	K562	blood:
10	chr2:55253298..55255265-chr2:55265294..55267097,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000200086	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10496038	1.00[MEX][hapmap]
rs11677750	0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11686912	1.00[MEX][hapmap]
rs11696046	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs11894868	1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13021245	1.00[CHB][hapmap];1.00[MEX][hapmap]
rs13030462	1.00[CHB][hapmap]
rs13032294	1.00[MEX][hapmap]
rs13033042	0.85[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs35125350	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6742306	1.00[MEX][hapmap]
rs7595814	1.00[MEX][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55237600-55258600	Weak transcription	Ovary	ovary
3	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
4	chr2:55241000-55272400	Weak transcription	Fetal Kidney	kidney
5	chr2:55242400-55258000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:55243000-55262400	Weak transcription	Hela-S3	cervix
7	chr2:55243800-55259800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:55245000-55256000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:55245600-55265600	Weak transcription	Stomach Mucosa	stomach
10	chr2:55246800-55259800	Weak transcription	NH-A	brain
11	chr2:55248200-55255200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:55248200-55255200	Weak transcription	Left Ventricle	heart
13	chr2:55248200-55258400	Weak transcription	Lung	lung
14	chr2:55248200-55259200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr2:55248600-55256400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:55249000-55256200	Enhancers	Primary T helper naive cells from peripheral blood	blood
17	chr2:55249000-55256600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:55249000-55256600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr2:55249000-55256600	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr2:55249000-55256600	Enhancers	Primary T helper cells fromperipheralblood	blood
21	chr2:55249200-55255000	Strong transcription	Dnd41	blood
22	chr2:55249200-55256600	Enhancers	Brain Angular Gyrus	brain
23	chr2:55249400-55254800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr2:55249400-55254800	Genic enhancers	Brain Anterior Caudate	brain
25	chr2:55249400-55255200	Weak transcription	Brain Germinal Matrix	brain
26	chr2:55249400-55256400	Enhancers	Adipose Nuclei	Adipose
27	chr2:55249600-55254400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr2:55249800-55255200	Enhancers	Primary neutrophils fromperipheralblood	blood
29	chr2:55249800-55255200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:55249800-55255800	Enhancers	Monocytes-CD14+_RO01746	blood
31	chr2:55250000-55256000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:55250000-55256400	Enhancers	Colon Smooth Muscle	Colon
33	chr2:55250000-55260000	Weak transcription	Gastric	stomach
34	chr2:55250200-55254400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:55250200-55255000	Weak transcription	Fetal Brain Male	brain
36	chr2:55250200-55256400	Enhancers	Rectal Smooth Muscle	rectum
37	chr2:55250400-55254800	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr2:55250400-55255000	Genic enhancers	Muscle Satellite Cultured Cells	--
39	chr2:55250400-55271000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr2:55250400-55274000	Weak transcription	Pancreas	Pancrea
41	chr2:55250600-55254600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr2:55250600-55258400	Weak transcription	Spleen	Spleen
43	chr2:55251200-55254600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr2:55251200-55254600	Enhancers	Primary B cells from peripheral blood	blood
45	chr2:55251200-55254800	Genic enhancers	HMEC	breast
46	chr2:55251200-55255400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr2:55251400-55254600	Enhancers	Primary B cells from cord blood	blood
48	chr2:55251400-55254800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:55251400-55254800	Genic enhancers	NHDF-Ad	bronchial
50	chr2:55251400-55258000	Weak transcription	Fetal Heart	heart

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