Variant report

Variant	rs17381453
Chromosome Location	chr1:160514987-160514988
allele	A/C
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	chr1:160514566..160515087-chr1:160576968..160577551,2	MCF-7	breast:
3	chr1:160514285..160515083-chr1:160576553..160577497,2	K562	blood:
4	chr1:160398077..160399076-chr1:160514554..160515127,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000066294	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1055880	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs11265442	0.81[CEU][hapmap]
rs11265452	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs11577695	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11583402	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11585738	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11590035	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12144628	0.81[CEU][hapmap]
rs12402879	0.81[CEU][hapmap]
rs12728784	0.83[CEU][hapmap]
rs1394078	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs151607	0.88[CEU][hapmap]
rs1572382	0.81[CEU][hapmap]
rs16832283	0.96[CEU][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs17385337	0.92[CEU][hapmap];0.86[GIH][hapmap];0.86[TSI][hapmap]
rs17385407	1.00[CEU][hapmap];0.82[GIH][hapmap];0.86[TSI][hapmap]
rs17385878	0.80[EUR][1000 genomes]
rs1809963	0.96[CEU][hapmap]
rs1998651	0.81[CEU][hapmap]
rs2025517	0.80[CEU][hapmap]
rs2083128	0.87[CEU][hapmap]
rs2099604	0.86[CEU][hapmap]
rs2753260	0.88[CEU][hapmap];1.00[MEX][hapmap]
rs3733264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3733265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3733266	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs3753381	0.86[MEX][hapmap]
rs3755898	0.83[EUR][1000 genomes]
rs3766384	0.83[EUR][1000 genomes]
rs3766385	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766387	0.95[CEU][hapmap];0.83[EUR][1000 genomes]
rs3766388	0.96[CEU][hapmap]
rs3766389	1.00[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs3816146	0.84[CEU][hapmap]
rs4145897	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5002947	0.96[CEU][hapmap];0.87[TSI][hapmap]
rs56040770	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61801562	0.84[EUR][1000 genomes]
rs61801564	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61801565	0.88[EUR][1000 genomes]
rs61801567	0.88[EUR][1000 genomes]
rs61802603	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61802604	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61802605	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61802606	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61802608	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61802610	0.93[ASN][1000 genomes]
rs6662093	0.86[EUR][1000 genomes]
rs6668760	0.81[CEU][hapmap]
rs6670721	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6687641	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs6692382	0.81[CEU][hapmap]
rs6697596	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6699346	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67197441	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72708818	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72708832	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7418241	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7539982	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7547054	0.88[CEU][hapmap]
rs7550771	0.88[CEU][hapmap];1.00[MEX][hapmap]
rs912582	1.00[CEU][hapmap]
rs977019	0.81[CEU][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	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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs17381453	ADAMTS4	cis	parietal	SCAN
rs17381453	VANGL2	cis	cerebellum	SCAN
rs17381453	KCNN3	cis	cerebellum	SCAN
rs17381453	OLFML2B	cis	parietal	SCAN
rs17381453	CD84	cis	lymphoblastoid	seeQTL
rs17381453	SLAMF6	cis	lymphoblastoid	seeQTL
rs17381453	NHLH1	cis	cerebellum	SCAN
rs17381453	ADAMTS4	cis	cerebellum	SCAN
rs17381453	CD84	Cis_1M	lymphoblastoid	RTeQTL
rs17381453	LRP1B	trans	parietal	SCAN
rs17381453	ATF6	cis	parietal	SCAN

Chromatin state (count:43 , 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	chr1:160510200-160515000	Enhancers	Stomach Mucosa	stomach
4	chr1:160510200-160520400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:160510600-160515000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr1:160510600-160515600	Enhancers	Fetal Thymus	thymus
7	chr1:160510600-160516000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:160510600-160516200	Weak transcription	Placenta	Placenta
9	chr1:160510800-160515400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:160511000-160515200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:160511000-160515400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr1:160511800-160517800	Weak transcription	Pancreas	Pancrea
13	chr1:160511800-160522400	Weak transcription	Gastric	stomach
14	chr1:160511800-160527800	Weak transcription	Colonic Mucosa	Colon
15	chr1:160512200-160524600	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr1:160512800-160516400	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr1:160513200-160516000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr1:160513200-160516800	Weak transcription	Fetal Lung	lung
19	chr1:160513400-160515200	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr1:160513400-160516000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:160513600-160515200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr1:160513800-160515000	Enhancers	Primary T cells fromperipheralblood	blood
23	chr1:160513800-160515000	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr1:160513800-160515200	Enhancers	Primary T cells from cord blood	blood
25	chr1:160513800-160516800	Enhancers	Primary B cells from peripheral blood	blood
26	chr1:160514000-160515000	Enhancers	Primary B cells from cord blood	blood
27	chr1:160514000-160515000	Enhancers	A549	lung
28	chr1:160514200-160515200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr1:160514200-160515200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:160514200-160515200	Enhancers	Primary T killer memory cells from peripheral blood	blood
31	chr1:160514200-160515200	Enhancers	Liver	Liver
32	chr1:160514200-160515400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr1:160514400-160515200	Enhancers	Thymus	Thymus
34	chr1:160514400-160515200	Enhancers	HepG2	liver
35	chr1:160514400-160519800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr1:160514600-160515000	Enhancers	Dnd41	blood
37	chr1:160514600-160515400	Enhancers	GM12878-XiMat	blood
38	chr1:160514600-160516200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr1:160514800-160515000	Enhancers	Duodenum Mucosa	Duodenum
40	chr1:160514800-160515200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
41	chr1:160514800-160515400	ZNF genes & repeats	K562	blood
42	chr1:160514800-160516000	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr1:160514800-160516400	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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