Variant report

Variant	rs41276257
Chromosome Location	chr5:95115959-95115960
allele	C/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	CTCF	chr5:95115757-95117524	SK-N-SH	brain:	n/a	chr5:95116910-95116928 chr5:95116913-95116926 chr5:95116912-95116933
2	POLR2A	chr5:95101625-95118213	K562	blood:	n/a	n/a
3	POLR2A	chr5:95111953-95118472	MCF-7	breast:	n/a	n/a
4	POLR2A	chr5:95115433-95116488	K562	blood:	n/a	n/a
5	MXI1	chr5:95115301-95115971	IMR90	lung:	n/a	n/a
6	GATA3	chr5:95115909-95116302	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:95113819..95116379-chr5:95117901..95121745,4	K562	blood:
2	chr5:95113691..95116957-chr5:95119419..95122737,4	MCF-7	breast:
3	chr5:95115747..95117608-chr5:95119159..95121512,2	MCF-7	breast:

Variant related genes	Relation type
RHOBTB3	TF binding region
ENSG00000164292	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10515229	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12522843	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12522899	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9784676	0.80[EUR][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	nsv598955	chr5:94903453-95136019	Flanking Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830409	chr5:95006686-95204496	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95072800-95133400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr5:95083200-95122000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:95087800-95134000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:95096400-95125400	Weak transcription	Small Intestine	intestine
5	chr5:95096600-95117000	Weak transcription	Brain Angular Gyrus	brain
6	chr5:95096600-95129800	Weak transcription	Colonic Mucosa	Colon
7	chr5:95105000-95131800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr5:95105400-95116200	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr5:95105400-95116400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr5:95105600-95116600	Weak transcription	Colon Smooth Muscle	Colon
11	chr5:95105600-95119200	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:95105600-95119800	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:95105800-95119400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:95105800-95119400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr5:95105800-95119600	Weak transcription	Brain Germinal Matrix	brain
16	chr5:95105800-95122200	Weak transcription	Fetal Brain Female	brain
17	chr5:95106400-95127400	Weak transcription	Fetal Brain Male	brain
18	chr5:95107200-95122400	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr5:95107400-95117000	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:95107400-95117000	Weak transcription	Stomach Smooth Muscle	stomach
21	chr5:95107600-95117000	Weak transcription	Fetal Kidney	kidney
22	chr5:95109600-95116000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr5:95109600-95116600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr5:95109600-95116600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr5:95109600-95116600	Weak transcription	Dnd41	blood
26	chr5:95109600-95117000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr5:95109600-95120400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr5:95109600-95123800	Weak transcription	HepG2	liver
29	chr5:95109800-95117000	Weak transcription	Brain Anterior Caudate	brain
30	chr5:95109800-95117000	Weak transcription	GM12878-XiMat	blood
31	chr5:95110400-95120200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr5:95111800-95116600	Strong transcription	Fetal Intestine Large	intestine
33	chr5:95111800-95117400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr5:95111800-95120800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:95112200-95118200	Strong transcription	Fetal Muscle Trunk	muscle
36	chr5:95112400-95116400	Strong transcription	Fetal Muscle Leg	muscle
37	chr5:95113000-95116600	Strong transcription	Fetal Intestine Small	intestine
38	chr5:95113400-95116400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr5:95114400-95116000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr5:95114400-95116200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:95114400-95116200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr5:95114400-95116600	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr5:95114400-95116800	Genic enhancers	Osteobl	bone
44	chr5:95114400-95117000	Genic enhancers	NHLF	lung
45	chr5:95114400-95117200	Enhancers	Primary hematopoietic stem cells	blood
46	chr5:95114400-95117200	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr5:95114400-95117400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:95114400-95118400	Genic enhancers	Placenta	Placenta
49	chr5:95114600-95116000	Enhancers	NHDF-Ad	bronchial
50	chr5:95114800-95116200	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links