Variant report

Variant	rs9400320
Chromosome Location	chr6:110065721-110065722
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11751112	0.81[TSI][hapmap]
rs11968485	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs12171561	0.98[ASN][1000 genomes]
rs12215867	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs13437149	0.81[JPT][hapmap]
rs1406957	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs1474959	0.81[ASW][hapmap];0.85[TSI][hapmap]
rs17612996	0.82[CEU][hapmap]
rs2145144	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs2224550	0.90[MKK][hapmap];0.84[YRI][hapmap]
rs2295836	0.81[JPT][hapmap]
rs2357128	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs2357226	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3823235	0.80[JPT][hapmap]
rs4523125	0.85[TSI][hapmap]
rs4946992	0.85[TSI][hapmap]
rs6568598	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6568600	0.87[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6568602	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6568603	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6941360	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7450970	0.85[TSI][hapmap]
rs7744981	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs7745469	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs7749910	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs7758697	0.98[ASN][1000 genomes]
rs829813	0.80[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.85[TSI][hapmap]
rs829814	0.82[CEU][hapmap];0.95[CHB][hapmap]
rs829816	0.85[TSI][hapmap]
rs9372226	0.81[JPT][hapmap]
rs9374095	0.81[CEU][hapmap]
rs9374097	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs9374110	0.84[CEU][hapmap]
rs9374114	0.81[CEU][hapmap]
rs9374121	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]
rs9384717	0.82[CEU][hapmap];0.95[CHB][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap]
rs9386813	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs9386824	0.85[TSI][hapmap]
rs9386826	0.91[CEU][hapmap]
rs9386839	0.91[ASN][1000 genomes]
rs9400310	0.80[MEX][hapmap];0.84[TSI][hapmap]
rs9400316	0.85[TSI][hapmap]
rs9480973	0.81[CEU][hapmap]
rs9480984	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs9480991	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs9481003	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9487172	0.85[TSI][hapmap]
rs9487176	0.80[MEX][hapmap];0.85[TSI][hapmap]
rs9487202	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9986507	0.82[ASW][hapmap];0.80[MEX][hapmap];0.85[TSI][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	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	nsv817322	chr6:109933272-110070574	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv830769	chr6:109944334-110078120	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9400320	SMPD2	cis	cerebellum	SCAN
rs9400320	FLJ42177	cis	multi-tissue	Pritchard
rs9400320	SMPD2	cis	Whole Blood	GTEx

Chromatin state (count:104 , 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	chr6:110028000-110071200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:110028200-110080800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr6:110035000-110071400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr6:110035000-110084000	Weak transcription	GM12878-XiMat	blood
6	chr6:110035200-110094200	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr6:110035400-110083000	Weak transcription	Brain Germinal Matrix	brain
8	chr6:110035600-110089000	Weak transcription	Spleen	Spleen
9	chr6:110036800-110115600	Weak transcription	Colonic Mucosa	Colon
10	chr6:110039000-110081000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
11	chr6:110041400-110081000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr6:110042200-110088800	Weak transcription	Fetal Intestine Small	intestine
13	chr6:110042400-110089000	Weak transcription	Brain Cingulate Gyrus	brain
14	chr6:110044200-110115400	Weak transcription	Brain Angular Gyrus	brain
15	chr6:110047000-110067200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr6:110047200-110084000	Weak transcription	Small Intestine	intestine
17	chr6:110047600-110068800	Weak transcription	Dnd41	blood
18	chr6:110048600-110089800	Weak transcription	Fetal Kidney	kidney
19	chr6:110050400-110065800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:110050400-110078400	Weak transcription	Fetal Brain Male	brain
21	chr6:110056000-110066600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr6:110056800-110067400	Weak transcription	Fetal Lung	lung
23	chr6:110057200-110089000	Weak transcription	Fetal Brain Female	brain
24	chr6:110057400-110089000	Weak transcription	Esophagus	oesophagus
25	chr6:110057600-110086200	Weak transcription	Brain Anterior Caudate	brain
26	chr6:110058200-110087200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr6:110058200-110089000	Weak transcription	Lung	lung
28	chr6:110058400-110085000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr6:110058400-110089600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr6:110058800-110112400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr6:110059200-110066400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr6:110059200-110067000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:110059200-110069400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:110059200-110124000	Weak transcription	Colon Smooth Muscle	Colon
35	chr6:110059800-110065800	Strong transcription	Adipose Nuclei	Adipose
36	chr6:110060000-110087800	Weak transcription	Fetal Thymus	thymus
37	chr6:110060400-110068000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr6:110061200-110089200	Weak transcription	Pancreas	Pancrea
39	chr6:110062000-110066200	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr6:110062400-110066400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr6:110062400-110067200	Weak transcription	Psoas Muscle	Psoas
42	chr6:110062600-110065800	Strong transcription	Primary B cells from cord blood	blood
43	chr6:110062600-110089200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr6:110062800-110087400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr6:110062800-110088000	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr6:110063000-110078000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr6:110063400-110065800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr6:110064200-110065800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr6:110064200-110065800	Strong transcription	Duodenum Mucosa	Duodenum
50	chr6:110064400-110065800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links