Variant report

Variant	rs7077388
Chromosome Location	chr10:45408658-45408659
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	chr10:45406784..45409410-chr10:45454257..45456258,2	K562	blood:
2	chr10:45402937..45405855-chr10:45407880..45411438,3	K562	blood:

Variant related genes	Relation type
ENSG00000224812	Chromatin interaction
ENSG00000273363	Chromatin interaction
ENSG00000107551	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10793568	0.81[YRI][hapmap]
rs10900131	1.00[CEU][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11239278	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11239282	0.94[JPT][hapmap];0.80[ASN][1000 genomes]
rs1332622	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2065465	1.00[CEU][hapmap];0.88[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs4543933	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6593448	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7082940	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7085840	1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7095112	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs7098274	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7477198	0.83[JPT][hapmap]
rs7911339	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs932986	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][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	nsv517161	chr10:45210690-45416256	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv831845	chr10:45300268-45460395	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv831846	chr10:45322236-45556370	Bivalent Enhancer Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv466909	chr10:45408011-45446791	Enhancers Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv550714	chr10:45408011-45446791	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7077388	RASGEF1A	cis	cerebellum	SCAN
rs7077388	ZNF488	cis	parietal	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:45401400-45415600	Weak transcription	Fetal Brain Female	brain
2	chr10:45401600-45410200	Enhancers	Fetal Muscle Leg	muscle
3	chr10:45403200-45409000	Enhancers	Fetal Thymus	thymus
4	chr10:45403800-45410000	Enhancers	Pancreas	Pancrea
5	chr10:45404000-45408800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr10:45404600-45409400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr10:45405800-45409000	Enhancers	Primary neutrophils fromperipheralblood	blood
8	chr10:45406200-45408800	Enhancers	Fetal Heart	heart
9	chr10:45406400-45408800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr10:45406400-45409000	Enhancers	K562	blood
11	chr10:45406400-45419000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr10:45406600-45408800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr10:45406600-45409000	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr10:45406600-45409400	Active TSS	Fetal Kidney	kidney
15	chr10:45406600-45410000	Enhancers	Lung	lung
16	chr10:45407200-45408800	Weak transcription	Fetal Lung	lung
17	chr10:45407200-45409000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr10:45407200-45410000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr10:45407200-45411600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr10:45407400-45409000	Enhancers	Primary hematopoietic stem cells	blood
21	chr10:45407400-45409400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr10:45407600-45408800	Weak transcription	Fetal Intestine Small	intestine
23	chr10:45407600-45408800	Weak transcription	Gastric	stomach
24	chr10:45407600-45408800	Weak transcription	Spleen	Spleen
25	chr10:45407600-45409400	Weak transcription	Fetal Intestine Large	intestine
26	chr10:45407600-45409400	Enhancers	Fetal Muscle Trunk	muscle
27	chr10:45407600-45409400	Weak transcription	Right Ventricle	heart
28	chr10:45407600-45411400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr10:45407800-45408800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr10:45407800-45408800	Enhancers	Primary B cells from cord blood	blood
31	chr10:45407800-45409000	Enhancers	Primary T cells from cord blood	blood
32	chr10:45407800-45409000	Weak transcription	Adipose Nuclei	Adipose
33	chr10:45407800-45422800	Weak transcription	Ovary	ovary
34	chr10:45408000-45409400	Weak transcription	Colonic Mucosa	Colon
35	chr10:45408000-45410000	Enhancers	Thymus	Thymus
36	chr10:45408200-45408800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr10:45408200-45409600	Enhancers	Left Ventricle	heart
38	chr10:45408200-45410000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr10:45408200-45410000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr10:45408200-45410200	Enhancers	Primary T helper naive cells from peripheral blood	blood
41	chr10:45408200-45410200	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr10:45408200-45410400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr10:45408200-45410400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr10:45408400-45409000	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr10:45408400-45409000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr10:45408400-45409400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr10:45408400-45409400	Enhancers	Placenta	Placenta
48	chr10:45408400-45409600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr10:45408400-45409600	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr10:45408400-45409800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links