Variant report

Variant	rs337589
Chromosome Location	chr9:101496508-101496509
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:101492037..101494835-chr9:101495591..101497324,2	K562	blood:
2	chr9:101490049..101492032-chr9:101495969..101498022,2	MCF-7	breast:
3	chr9:101451350..101454293-chr9:101494298..101496976,2	MCF-7	breast:
4	chr9:101485653..101487563-chr9:101495414..101497916,2	K562	blood:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10119228	0.88[ASN][1000 genomes]
rs10125255	0.90[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs10512260	1.00[ASW][hapmap];0.96[LWK][hapmap];0.88[MKK][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes]
rs10739704	0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs10987843	0.88[ASN][1000 genomes]
rs11791408	1.00[ASW][hapmap];0.96[LWK][hapmap];1.00[MKK][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes]
rs1555520	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs1555522	0.90[CHB][hapmap];0.86[JPT][hapmap]
rs180038	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.94[ASN][1000 genomes]
rs180039	1.00[CEU][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182877	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1930132	0.89[AFR][1000 genomes]
rs1930423	0.82[GIH][hapmap]
rs2058881	0.86[ASN][1000 genomes]
rs2295922	0.95[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs337564	0.90[CHB][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs337565	0.90[CHB][hapmap];0.83[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs337566	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs337567	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs337568	0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs337570	0.86[CHB][hapmap];0.84[JPT][hapmap];0.92[ASN][1000 genomes]
rs337571	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs337580	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs337583	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs337585	0.90[CHB][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs337586	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs337587	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs337588	0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs337590	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs371521	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4133240	0.90[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs439347	0.90[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs453409	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4742740	0.85[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.92[MEX][hapmap];0.93[ASN][1000 genomes]
rs4742742	0.91[ASN][1000 genomes]
rs4743274	0.90[CHB][hapmap];0.86[JPT][hapmap];0.96[ASN][1000 genomes]
rs4743277	0.90[CHB][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.91[ASN][1000 genomes]
rs4743279	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4743280	0.90[CHB][hapmap];0.85[CHD][hapmap];0.84[JPT][hapmap];1.00[MEX][hapmap];0.91[ASN][1000 genomes]
rs48418	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs507318	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs57644057	0.92[AFR][1000 genomes]
rs57882865	0.94[AFR][1000 genomes]
rs61335015	0.94[AFR][1000 genomes]
rs61383603	0.93[AFR][1000 genomes]
rs6415847	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6415849	0.91[ASN][1000 genomes]
rs692824	0.90[CHB][hapmap];0.85[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[ASN][1000 genomes]
rs7029599	0.93[ASN][1000 genomes]
rs7039118	0.90[CHB][hapmap];0.90[ASN][1000 genomes]
rs73491756	0.81[AFR][1000 genomes]
rs73491783	0.89[AFR][1000 genomes]
rs73491789	0.93[AFR][1000 genomes]
rs73493922	0.96[AFR][1000 genomes]
rs754222	0.90[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs7846846	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7861840	0.95[CHB][hapmap];0.83[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[ASN][1000 genomes]
rs7867234	0.86[CHB][hapmap];0.93[ASN][1000 genomes]
rs7867317	0.93[ASN][1000 genomes]
rs9409306	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv614936	chr9:101182698-101680380	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv893614	chr9:101340316-101671634	Enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
3	nsv893615	chr9:101356515-101678036	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	esv2830198	chr9:101477500-101512140	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs337589	ICOS	trans	lymphoblastoid	seeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:101486400-101513000	Weak transcription	Right Atrium	heart
2	chr9:101489000-101496600	Weak transcription	Primary B cells from cord blood	blood
3	chr9:101489000-101497400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:101489000-101498200	Weak transcription	Brain Germinal Matrix	brain
5	chr9:101489200-101501000	Weak transcription	Primary hematopoietic stem cells	blood
6	chr9:101489400-101496800	Weak transcription	Brain Cingulate Gyrus	brain
7	chr9:101489400-101497200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr9:101489400-101498200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr9:101489600-101497000	Weak transcription	Brain Angular Gyrus	brain
10	chr9:101489600-101497800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr9:101489600-101497800	Weak transcription	Fetal Thymus	thymus
12	chr9:101489800-101520800	Weak transcription	Fetal Brain Male	brain
13	chr9:101490200-101497600	Weak transcription	Primary B cells from peripheral blood	blood
14	chr9:101490600-101497000	Weak transcription	HSMM	muscle
15	chr9:101491000-101504400	Weak transcription	A549	lung
16	chr9:101491000-101505800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:101491000-101518000	Weak transcription	Thymus	Thymus
18	chr9:101492800-101496800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr9:101492800-101499400	Strong transcription	Fetal Intestine Small	intestine
20	chr9:101492800-101505800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:101493000-101496600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr9:101493000-101496800	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr9:101493000-101496800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr9:101493000-101497400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr9:101493000-101498400	Weak transcription	NHLF	lung
26	chr9:101493000-101507400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr9:101493400-101496800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr9:101493400-101504400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr9:101493600-101496600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr9:101493600-101497200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr9:101493600-101497400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr9:101494000-101497400	Weak transcription	Fetal Lung	lung
33	chr9:101494000-101532600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr9:101494000-101535200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr9:101494200-101497400	Weak transcription	Left Ventricle	heart
36	chr9:101494200-101501200	Weak transcription	K562	blood
37	chr9:101494200-101505600	Weak transcription	Colon Smooth Muscle	Colon
38	chr9:101494200-101509000	Strong transcription	Primary T cells from cord blood	blood
39	chr9:101494200-101516800	Weak transcription	Psoas Muscle	Psoas
40	chr9:101494400-101499000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr9:101494400-101499400	Strong transcription	Fetal Stomach	stomach
42	chr9:101494400-101499400	Strong transcription	Stomach Smooth Muscle	stomach
43	chr9:101494400-101553000	Weak transcription	Fetal Heart	heart
44	chr9:101494600-101497800	Weak transcription	NHDF-Ad	bronchial
45	chr9:101494600-101498000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr9:101494600-101520800	Weak transcription	Fetal Kidney	kidney
47	chr9:101494800-101496800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr9:101494800-101506200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr9:101495000-101498000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr9:101495000-101498200	Weak transcription	iPS-15b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links