Variant report

Variant	rs10918281
Chromosome Location	chr1:165734088-165734089
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:165732937..165734507-chr1:167189047..167191428,2	MCF-7	breast:
2	chr1:165733730..165736417-chr1:165798667..165800425,2	K562	blood:
3	chr1:165730442..165735280-chr1:165736024..165740207,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272205	Chromatin interaction
ENSG00000224358	Chromatin interaction
ENSG00000143183	Chromatin interaction
ENSG00000143190	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10800152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10918276	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12127304	0.84[ASN][1000 genomes]
rs12723198	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs14223	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1913846	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs1999992	0.85[CHB][hapmap]
rs2814470	0.90[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs28475591	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3186873	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4366297	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4656462	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4657470	0.86[CHB][hapmap];0.88[CHD][hapmap]
rs6426937	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs6426940	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs6656194	0.90[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap]
rs6679238	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7411708	0.90[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2756102	chr1:165652342-165877342	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1011720	chr1:165669589-165802516	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv518886	chr1:165714187-165741646	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10918281	FCGR3A	cis	parietal	SCAN
rs10918281	VANGL2	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:165687600-165737600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:165694600-165736800	Strong transcription	Monocytes-CD14+_RO01746	blood
3	chr1:165711200-165736200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:165712200-165737000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:165712600-165737000	Weak transcription	Colonic Mucosa	Colon
6	chr1:165713600-165737000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:165721800-165734800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:165721800-165734800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:165721800-165734800	Weak transcription	Esophagus	oesophagus
10	chr1:165721800-165735200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:165721800-165736600	Weak transcription	Stomach Mucosa	stomach
12	chr1:165721800-165737000	Weak transcription	Fetal Brain Male	brain
13	chr1:165721800-165737000	Weak transcription	Fetal Heart	heart
14	chr1:165721800-165737000	Weak transcription	Right Atrium	heart
15	chr1:165721800-165737200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr1:165721800-165737600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:165722400-165735000	Weak transcription	HSMMtube	muscle
18	chr1:165722600-165736800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr1:165722800-165734800	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:165723000-165736800	Weak transcription	Spleen	Spleen
21	chr1:165723200-165736800	Weak transcription	Colon Smooth Muscle	Colon
22	chr1:165723400-165734800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:165723600-165735600	Weak transcription	Brain Germinal Matrix	brain
24	chr1:165725800-165734200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr1:165726400-165736800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:165726800-165736800	Strong transcription	Primary monocytes fromperipheralblood	blood
27	chr1:165726800-165737000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr1:165727000-165736800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:165727600-165734200	Weak transcription	Fetal Lung	lung
30	chr1:165727600-165735000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:165727600-165735000	Weak transcription	Aorta	Aorta
32	chr1:165727800-165735400	Weak transcription	Right Ventricle	heart
33	chr1:165727800-165737000	Weak transcription	Psoas Muscle	Psoas
34	chr1:165727800-165737600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr1:165729200-165734200	Weak transcription	Fetal Kidney	kidney
36	chr1:165729200-165737200	Weak transcription	Brain Substantia Nigra	brain
37	chr1:165730200-165736800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr1:165730200-165736800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:165730200-165736800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr1:165730400-165736600	Strong transcription	HSMM	muscle
41	chr1:165730400-165736800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr1:165730400-165736800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:165730600-165736600	Strong transcription	Hela-S3	cervix
44	chr1:165731200-165734400	Weak transcription	Fetal Stomach	stomach
45	chr1:165731200-165734600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr1:165731200-165734600	Weak transcription	Fetal Intestine Small	intestine
47	chr1:165731200-165734600	Weak transcription	Lung	lung
48	chr1:165731200-165734800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr1:165731200-165736800	Weak transcription	Gastric	stomach
50	chr1:165731400-165735000	Weak transcription	Fetal Intestine Large	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links