Variant report

Variant	rs4145897
Chromosome Location	chr1:160513173-160513174
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:160509002..160516145-chr1:160518936..160522666,8	K562	blood:
2	chr1:160510180..160511755-chr1:160511798..160513582,2	MCF-7	breast:
3	chr1:160512749..160514411-chr1:160517528..160520237,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066294	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1055880	0.87[EUR][1000 genomes]
rs11265424	0.83[EUR][1000 genomes]
rs11577695	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11583402	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11585738	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11590035	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1394078	0.81[EUR][1000 genomes]
rs17381453	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733264	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3733265	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3733266	0.87[EUR][1000 genomes]
rs3755898	0.81[EUR][1000 genomes]
rs3766384	0.81[EUR][1000 genomes]
rs3766385	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766387	0.81[EUR][1000 genomes]
rs3766389	0.86[EUR][1000 genomes]
rs56040770	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61801562	0.81[EUR][1000 genomes]
rs61801564	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61801565	0.85[EUR][1000 genomes]
rs61801567	0.85[EUR][1000 genomes]
rs61802603	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61802604	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61802605	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61802606	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61802608	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61802610	0.93[ASN][1000 genomes]
rs6662093	0.82[EUR][1000 genomes]
rs6670721	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6697596	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6699346	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67197441	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72708818	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72708832	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7418241	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7539982	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]

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	esv1829614	chr1:160465291-160595000	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv872491	chr1:160470258-160580549	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv831703	chr1:160496124-160643024	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4145897	CD84	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160507600-160515400	Enhancers	Fetal Intestine Large	intestine
2	chr1:160507800-160515400	Enhancers	Fetal Intestine Small	intestine
3	chr1:160508400-160513200	Enhancers	Primary hematopoietic stem cells	blood
4	chr1:160508600-160513200	Enhancers	Liver	Liver
5	chr1:160509800-160513200	Enhancers	Fetal Lung	lung
6	chr1:160510200-160515000	Enhancers	Stomach Mucosa	stomach
7	chr1:160510200-160520400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:160510400-160513200	Enhancers	Duodenum Mucosa	Duodenum
9	chr1:160510600-160515000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:160510600-160515600	Enhancers	Fetal Thymus	thymus
11	chr1:160510600-160516000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:160510600-160516200	Weak transcription	Placenta	Placenta
13	chr1:160510800-160513200	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:160510800-160513200	Enhancers	Thymus	Thymus
15	chr1:160510800-160513200	Enhancers	GM12878-XiMat	blood
16	chr1:160510800-160513400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr1:160510800-160515400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr1:160511000-160515200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:160511000-160515400	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr1:160511200-160513400	Enhancers	K562	blood
21	chr1:160511600-160514400	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr1:160511600-160514800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr1:160511800-160514000	Weak transcription	Primary B cells from cord blood	blood
24	chr1:160511800-160517800	Weak transcription	Pancreas	Pancrea
25	chr1:160511800-160522400	Weak transcription	Gastric	stomach
26	chr1:160511800-160527800	Weak transcription	Colonic Mucosa	Colon
27	chr1:160512000-160513800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr1:160512000-160513800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr1:160512000-160513800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr1:160512000-160514600	Weak transcription	Dnd41	blood
31	chr1:160512200-160513600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr1:160512200-160513600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:160512200-160514200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr1:160512200-160524600	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr1:160512400-160514800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr1:160512600-160513600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:160512600-160513800	Weak transcription	Primary T cells from cord blood	blood
38	chr1:160512600-160513800	Weak transcription	Primary T helper cells fromperipheralblood	blood
39	chr1:160512600-160514200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr1:160512800-160514200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
41	chr1:160512800-160516400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:160513000-160513400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr1:160513000-160513600	Enhancers	A549	lung
44	chr1:160513000-160514400	Weak transcription	HepG2	liver
45	chr1:160513000-160514600	Enhancers	Small Intestine	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links