Variant report

Variant	rs9374121
Chromosome Location	chr6:110092054-110092055
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10872052	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs11153200	0.80[CEU][hapmap];0.92[CHB][hapmap]
rs11751112	0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs11757485	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs11759958	0.85[EUR][1000 genomes]
rs11968485	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs12215867	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap]
rs12524352	0.91[CHB][hapmap]
rs1321327	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs13437149	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1406957	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs1474959	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs1570013	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs17070874	0.92[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs17612758	0.81[CEU][hapmap];0.85[EUR][1000 genomes]
rs17612996	0.85[CEU][hapmap];0.86[EUR][1000 genomes]
rs2016207	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs2076929	0.90[CHB][hapmap]
rs2145144	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs2295835	0.92[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs2295836	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2357128	0.88[TSI][hapmap]
rs2357226	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3823235	0.92[CHB][hapmap];0.94[JPT][hapmap]
rs4523125	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap]
rs4946992	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.90[TSI][hapmap]
rs56009458	0.86[EUR][1000 genomes]
rs58068940	0.86[EUR][1000 genomes]
rs62437568	0.86[EUR][1000 genomes]
rs6568587	0.83[CHB][hapmap]
rs6568595	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs6568600	0.88[TSI][hapmap]
rs6568602	0.84[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes]
rs6568603	0.85[MEX][hapmap];0.90[TSI][hapmap]
rs6568604	0.84[EUR][1000 genomes]
rs6917383	0.83[CHB][hapmap]
rs6924269	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs6925005	0.83[CHB][hapmap]
rs6941360	0.96[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73535341	0.85[ASN][1000 genomes]
rs7356790	0.83[CHB][hapmap]
rs7450970	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap]
rs7453835	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs7742066	0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs7744981	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap]
rs7745469	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs7749605	0.81[CHB][hapmap]
rs7749910	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs7756284	0.81[CEU][hapmap];0.86[EUR][1000 genomes]
rs7761008	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs7765916	0.83[CHB][hapmap]
rs7772938	0.86[EUR][1000 genomes]
rs7775092	0.93[ASN][1000 genomes]
rs829813	0.85[TSI][hapmap]
rs829816	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap]
rs9320304	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs9372221	0.81[CEU][hapmap]
rs9372222	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs9372225	0.90[ASN][1000 genomes]
rs9372226	0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9374108	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs9374110	0.87[CEU][hapmap];0.88[CHB][hapmap]
rs9374114	0.84[CEU][hapmap];0.92[CHB][hapmap]
rs9374117	0.93[ASN][1000 genomes]
rs9384717	0.88[TSI][hapmap]
rs9386818	0.83[CEU][hapmap];0.91[CHB][hapmap]
rs9386823	0.91[CHB][hapmap]
rs9386824	0.89[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap]
rs9386826	0.95[CEU][hapmap];0.89[CHB][hapmap]
rs9386835	0.92[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs9386842	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9398214	0.92[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs9398215	0.92[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs9400310	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs9400312	0.81[CEU][hapmap];0.91[CHB][hapmap]
rs9400313	0.83[CHB][hapmap]
rs9400316	0.89[ASW][hapmap];0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.83[YRI][hapmap]
rs9400320	0.96[CEU][hapmap];0.82[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9480984	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs9480991	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs9481003	0.81[JPT][hapmap]
rs9487171	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs9487172	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs9487175	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs9487176	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap]
rs9487180	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs9487193	0.85[ASN][1000 genomes]
rs9487202	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9487203	0.93[ASN][1000 genomes]
rs971432	0.81[CEU][hapmap];0.92[CHB][hapmap]
rs9986507	0.81[CEU][hapmap];0.92[CHB][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.90[TSI][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	nsv949475	chr6:109907936-110160501	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv5436	chr6:110052812-110097662	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv886533	chr6:110067773-110126393	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9374121	SMPD2	cis	Whole Blood	GTEx
rs9374121	SMPD2	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:110013000-110114400	Weak transcription	Right Ventricle	heart
2	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr6:110036800-110115600	Weak transcription	Colonic Mucosa	Colon
4	chr6:110044200-110115400	Weak transcription	Brain Angular Gyrus	brain
5	chr6:110058800-110112400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr6:110059200-110124000	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:110065200-110111200	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr6:110065400-110094200	Weak transcription	Brain Substantia Nigra	brain
9	chr6:110065800-110107400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr6:110065800-110107400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr6:110078800-110107400	Weak transcription	Fetal Brain Male	brain
12	chr6:110081200-110094200	Weak transcription	Psoas Muscle	Psoas
13	chr6:110081200-110109600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr6:110081600-110092200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr6:110081600-110115000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr6:110081800-110093400	Weak transcription	Hela-S3	cervix
17	chr6:110082000-110152600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr6:110082200-110119800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr6:110084200-110115400	Weak transcription	Small Intestine	intestine
20	chr6:110084400-110094000	Weak transcription	Stomach Mucosa	stomach
21	chr6:110084400-110094200	Weak transcription	HSMM	muscle
22	chr6:110084600-110094000	Weak transcription	Fetal Heart	heart
23	chr6:110085600-110112600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr6:110086400-110104600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr6:110086600-110093000	Weak transcription	HMEC	breast
26	chr6:110087200-110092800	Strong transcription	Primary T cells from cord blood	blood
27	chr6:110087600-110094000	Weak transcription	HSMMtube	muscle
28	chr6:110087600-110094200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr6:110087600-110094200	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr6:110088400-110107600	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:110089000-110107600	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:110089200-110093800	Weak transcription	Left Ventricle	heart
33	chr6:110089400-110111400	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr6:110089600-110094200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:110089600-110108000	Weak transcription	Brain Anterior Caudate	brain
36	chr6:110089600-110111400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr6:110089600-110115600	Weak transcription	Esophagus	oesophagus
38	chr6:110089600-110115600	Weak transcription	Gastric	stomach
39	chr6:110089800-110096600	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr6:110089800-110107200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr6:110089800-110107400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr6:110089800-110115200	Weak transcription	Brain Cingulate Gyrus	brain
43	chr6:110090000-110093000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr6:110090000-110093600	Enhancers	Primary B cells from cord blood	blood
45	chr6:110090000-110093800	Enhancers	GM12878-XiMat	blood
46	chr6:110090000-110094000	Weak transcription	Brain Hippocampus Middle	brain
47	chr6:110090000-110094200	Weak transcription	Adipose Nuclei	Adipose
48	chr6:110090000-110098000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr6:110090000-110098200	Weak transcription	Placenta	Placenta
50	chr6:110090000-110098400	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links