Variant report

Variant	rs4907076
Chromosome Location	chr1:84947055-84947056
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:84945634..84947258-chr1:85153889..85156502,2	K562	blood:
2	chr1:84946730..84947401-chr9:80911526..80912502,2	HCT-116	colon:
3	chr1:84943703..84948095-chr1:85037647..85043843,8	K562	blood:
4	chr1:84765808..84767323-chr1:84944913..84947326,2	K562	blood:
5	chr1:84946525..84949349-chr1:84951021..84952787,2	MCF-7	breast:
6	chr1:84944684..84947410-chr1:84970225..84973395,6	MCF-7	breast:
7	chr1:84940376..84943283-chr1:84945216..84947221,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117151	Chromatin interaction
ENSG00000122432	Chromatin interaction
ENSG00000135069	Chromatin interaction
ENSG00000203943	Chromatin interaction
ENSG00000117155	Chromatin interaction
ENSG00000174021	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11163971	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11163972	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11163981	0.84[CHD][hapmap]
rs11163992	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1123981	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1144276	0.84[CHD][hapmap]
rs11578494	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11586006	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12123381	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124568	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12124731	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12126584	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12126924	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128801	0.84[CHD][hapmap]
rs12136756	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12137559	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12140555	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12143652	0.85[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs12145405	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1246159	0.84[CHD][hapmap]
rs1395416	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1395417	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1506707	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17109982	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17110030	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17110519	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2271620	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.83[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2292191	0.82[CHD][hapmap]
rs2292808	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs312395	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs312397	0.84[CHD][hapmap]
rs3813605	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3813607	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3922538	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4907077	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56212819	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57245302	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57442052	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74095416	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs74095424	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74095432	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74095436	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7512922	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7513490	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7514763	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7519606	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7535445	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7536988	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs925740	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv830437	chr1:84837524-85001269	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4907076	ZSWIM1	trans	cerebellum	SCAN
rs4907076	SPATA1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:84945600-84949000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:84945800-84947200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr1:84946000-84947400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr1:84946000-84947400	Enhancers	Fetal Heart	heart
5	chr1:84946000-84947400	Enhancers	Small Intestine	intestine
6	chr1:84946000-84948600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:84946000-84949000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:84946000-84949000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr1:84946000-84956400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:84946000-84956400	Weak transcription	Gastric	stomach
11	chr1:84946000-84956400	Weak transcription	Spleen	Spleen
12	chr1:84946000-84965800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:84946000-84967000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:84946000-84969600	Weak transcription	Esophagus	oesophagus
15	chr1:84946000-84970400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:84946000-84970800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:84946200-84947200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr1:84946200-84947200	Flanking Active TSS	Hela-S3	cervix
19	chr1:84946200-84947400	Enhancers	Colon Smooth Muscle	Colon
20	chr1:84946200-84947600	Weak transcription	Brain Substantia Nigra	brain
21	chr1:84946200-84948600	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:84946200-84948600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr1:84946200-84949000	Weak transcription	Fetal Stomach	stomach
24	chr1:84946200-84949200	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:84946200-84955200	Weak transcription	Right Ventricle	heart
26	chr1:84946200-84956200	Weak transcription	Colonic Mucosa	Colon
27	chr1:84946200-84962800	Weak transcription	HSMMtube	muscle
28	chr1:84946400-84947200	Enhancers	Adipose Nuclei	Adipose
29	chr1:84946400-84947200	Enhancers	Liver	Liver
30	chr1:84946400-84947200	Enhancers	Brain Hippocampus Middle	brain
31	chr1:84946400-84947200	Enhancers	Fetal Intestine Large	intestine
32	chr1:84946400-84947200	Enhancers	Stomach Smooth Muscle	stomach
33	chr1:84946400-84947200	Enhancers	NHLF	lung
34	chr1:84946400-84947400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:84946400-84947400	Enhancers	Fetal Intestine Small	intestine
36	chr1:84946400-84947400	Enhancers	Rectal Smooth Muscle	rectum
37	chr1:84946400-84947400	Enhancers	NHEK	skin
38	chr1:84946400-84947600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:84946400-84947600	Enhancers	HepG2	liver
40	chr1:84946400-84947800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr1:84946400-84948000	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr1:84946400-84948200	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:84946400-84948600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr1:84946400-84948600	Weak transcription	Osteobl	bone
45	chr1:84946400-84948800	Enhancers	Primary T helper naive cells from peripheral blood	blood
46	chr1:84946400-84949000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:84946400-84949400	Weak transcription	NH-A	brain
48	chr1:84946400-84955200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:84946400-84955600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr1:84946400-84956200	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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