Variant report

Variant	rs9870740
Chromosome Location	chr3:150989323-150989324
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10212582	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1048408	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10513392	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11714714	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11717955	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11719936	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12330831	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12488267	0.91[ASN][1000 genomes]
rs12494865	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs1317465	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13317873	0.85[CEU][hapmap]
rs1352886	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1472122	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1565574	0.92[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs16863323	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs16863334	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs16863336	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1844924	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1882014	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1882015	0.93[CEU][hapmap];0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1882016	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1882017	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1920395	0.87[YRI][hapmap]
rs1920396	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1980143	0.96[CEU][hapmap]
rs28371419	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28497341	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2904430	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3846072	0.85[CEU][hapmap]
rs4076581	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4475010	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4679772	0.96[CEU][hapmap];0.81[AMR][1000 genomes]
rs4679783	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680254	0.89[CEU][hapmap]
rs4680257	0.96[CEU][hapmap]
rs4680260	0.89[CEU][hapmap]
rs4680273	0.85[CEU][hapmap];0.84[YRI][hapmap]
rs56367650	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58334126	0.84[ASN][1000 genomes]
rs62283021	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6440730	0.85[CEU][hapmap]
rs6765215	0.80[ASN][1000 genomes]
rs6768130	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6782313	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6782715	0.85[CEU][hapmap]
rs6807308	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6809692	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs73021201	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7617677	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7621113	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7621183	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7621211	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7623448	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7653603	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8180086	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9757688	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9810067	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9815520	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9827619	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9828553	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9829753	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9835328	0.86[CEU][hapmap]
rs9853297	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9875152	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9880339	0.85[CEU][hapmap]

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	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv979890	chr3:150986756-150990249	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150977800-151000000	Weak transcription	Placenta	Placenta
2	chr3:150981800-150994000	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:150983000-151011000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:150983800-150989400	Enhancers	Primary B cells from cord blood	blood
5	chr3:150983800-151000600	Weak transcription	Brain Substantia Nigra	brain
6	chr3:150984000-150996000	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:150984200-150998800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr3:150984400-151022400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:150984600-151003600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:150984600-151003600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr3:150984800-150993800	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr3:150986000-150989800	Enhancers	Primary B cells from peripheral blood	blood
13	chr3:150986800-150991400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr3:150986800-150992200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:150986800-150992800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:150986800-150994000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:150987000-150991800	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:150987000-150992000	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr3:150987000-150992000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:150987000-150992000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr3:150987000-150992200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:150987200-150991800	Weak transcription	Fetal Thymus	thymus
23	chr3:150987400-150992600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:150987800-150990600	Weak transcription	GM12878-XiMat	blood
25	chr3:150987800-150991400	Weak transcription	Primary T cells from cord blood	blood
26	chr3:150987800-150992000	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr3:150987800-150993600	Weak transcription	Adipose Nuclei	Adipose
28	chr3:150988200-150993000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:150988600-150993600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr3:150988600-150995800	Weak transcription	Colon Smooth Muscle	Colon
31	chr3:150989000-150989600	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links