Variant report

Variant	rs9532001
Chromosome Location	chr13:37535810-37535811
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1199962	0.90[CEU][hapmap]
rs1199963	0.90[CEU][hapmap];1.00[LWK][hapmap];0.87[TSI][hapmap];0.82[AFR][1000 genomes]
rs1199974	0.90[CEU][hapmap]
rs1199981	0.90[CEU][hapmap]
rs1199982	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs1199983	0.90[CEU][hapmap]
rs1199984	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs12865199	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1543738	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs1764483	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs1924419	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1924420	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1924421	0.84[EUR][1000 genomes]
rs1924422	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1937761	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs2093817	0.90[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs2147169	1.00[CEU][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes]
rs2181787	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2181788	0.91[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs2186157	0.97[EUR][1000 genomes]
rs2323165	1.00[CEU][hapmap];0.85[GIH][hapmap];1.00[LWK][hapmap];0.89[MKK][hapmap];0.94[TSI][hapmap];0.88[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs2769543	0.80[CEU][hapmap]
rs2785620	0.90[CEU][hapmap];0.81[TSI][hapmap]
rs4291799	1.00[CEU][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes]
rs4624036	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs483304	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4941854	1.00[CEU][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs4941855	0.96[EUR][1000 genomes]
rs4941856	1.00[CEU][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs4943441	0.90[CEU][hapmap];0.85[GIH][hapmap];0.86[TSI][hapmap]
rs568992	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs587505	0.81[CEU][hapmap];1.00[GIH][hapmap];0.81[TSI][hapmap]
rs647421	0.93[AMR][1000 genomes]
rs6563506	0.91[CEU][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes]
rs6563507	1.00[CEU][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes]
rs6563508	0.90[CEU][hapmap];0.87[TSI][hapmap]
rs675108	0.82[CEU][hapmap]
rs688280	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs71432622	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7317750	1.00[CEU][hapmap];0.85[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs7321129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7329314	0.97[EUR][1000 genomes]
rs7334233	0.99[EUR][1000 genomes]
rs7338929	1.00[CEU][hapmap];0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs7982674	0.99[EUR][1000 genomes]
rs7983986	1.00[CEU][hapmap];0.85[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs7984730	0.94[EUR][1000 genomes]
rs7989205	1.00[CEU][hapmap];0.85[GIH][hapmap];0.94[TSI][hapmap];0.96[EUR][1000 genomes]
rs7989380	0.90[CEU][hapmap]
rs7991057	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7991181	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7997310	0.90[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs9315458	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9315459	0.99[EUR][1000 genomes]
rs9531998	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9532002	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9532004	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9532005	1.00[CEU][hapmap];0.94[TSI][hapmap];0.99[EUR][1000 genomes]
rs9547705	0.82[AMR][1000 genomes]
rs9547707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9547712	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9547715	1.00[CEU][hapmap];0.85[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs9547717	0.91[CEU][hapmap];0.83[TSI][hapmap];0.95[EUR][1000 genomes]
rs9547718	1.00[CEU][hapmap];0.85[GIH][hapmap];0.94[TSI][hapmap];0.97[EUR][1000 genomes]
rs9576153	0.99[EUR][1000 genomes]
rs9576154	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs9594181	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9603121	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948975	chr13:37281203-38280430	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv522336	chr13:37305641-37584838	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9532001	SUPT20H	cis	Whole Blood	GTEx
rs9532001	FAM48A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:37517200-37538400	Weak transcription	Fetal Brain Male	brain
2	chr13:37519600-37561400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:37520400-37538000	Weak transcription	Colonic Mucosa	Colon
4	chr13:37520600-37560800	Weak transcription	Small Intestine	intestine
5	chr13:37520800-37538000	Weak transcription	HepG2	liver
6	chr13:37521000-37536600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr13:37521200-37538200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr13:37521400-37537800	Weak transcription	NHLF	lung
9	chr13:37521400-37538000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr13:37521400-37538400	Weak transcription	Aorta	Aorta
11	chr13:37521400-37542800	Weak transcription	A549	lung
12	chr13:37521600-37537800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr13:37521600-37538000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr13:37521600-37538000	Weak transcription	Brain Hippocampus Middle	brain
15	chr13:37521600-37538200	Weak transcription	HSMMtube	muscle
16	chr13:37521800-37539200	Weak transcription	K562	blood
17	chr13:37522000-37538000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr13:37522000-37538400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr13:37522600-37541000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr13:37522600-37548800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr13:37522800-37547000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr13:37523000-37538400	Weak transcription	Lung	lung
23	chr13:37523000-37545600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr13:37523200-37558200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr13:37523400-37538000	Weak transcription	Brain Substantia Nigra	brain
26	chr13:37523400-37538000	Weak transcription	Esophagus	oesophagus
27	chr13:37523600-37536600	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr13:37523800-37536800	Weak transcription	Brain Germinal Matrix	brain
29	chr13:37523800-37538000	Weak transcription	Brain Anterior Caudate	brain
30	chr13:37524000-37563800	Weak transcription	Psoas Muscle	Psoas
31	chr13:37524600-37538400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr13:37524600-37572400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr13:37524800-37546400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr13:37525000-37560800	Weak transcription	Fetal Heart	heart
35	chr13:37525600-37544800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr13:37525800-37537400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr13:37526000-37538200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr13:37526200-37538000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr13:37526600-37536000	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr13:37526600-37536600	Weak transcription	Left Ventricle	heart
41	chr13:37526600-37537000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr13:37526600-37538000	Weak transcription	Brain Cingulate Gyrus	brain
43	chr13:37526600-37556200	Weak transcription	Brain Angular Gyrus	brain
44	chr13:37526800-37559400	Weak transcription	Hela-S3	cervix
45	chr13:37527200-37536600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr13:37527800-37538400	Weak transcription	Right Ventricle	heart
47	chr13:37528200-37537600	Weak transcription	Colon Smooth Muscle	Colon
48	chr13:37528200-37538200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr13:37528600-37538400	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr13:37528600-37541800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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