Variant report

Variant	rs9804056
Chromosome Location	chr1:174907168-174907169
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10436863	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1046439	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap]
rs11590474	1.00[LWK][hapmap]
rs12083837	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1653626	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap]
rs1653627	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.82[EUR][1000 genomes]
rs1653632	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.85[EUR][1000 genomes]
rs1754349	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1754351	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs1754355	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs1793297	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs1793300	0.81[EUR][1000 genomes]
rs1793309	0.87[EUR][1000 genomes]
rs1793319	0.82[CEU][hapmap];0.83[GIH][hapmap];0.80[MEX][hapmap]
rs1801791	0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap]
rs1984418	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap]
rs2105949	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap]
rs2187562	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2285210	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap]
rs2981894	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2987869	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs2987874	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs3018410	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3118980	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap]
rs3133270	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs332789	0.80[EUR][1000 genomes]
rs3753563	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs4233195	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs4650666	0.85[CEU][hapmap]
rs4651238	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55741955	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61828140	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61828142	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425305	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6425309	0.81[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap]
rs6425310	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap]
rs6656665	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6658861	0.82[CEU][hapmap];0.83[GIH][hapmap];0.84[MEX][hapmap]
rs6665216	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6669560	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap]
rs66700013	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6688577	0.84[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap]
rs7355181	0.84[TSI][hapmap]
rs7538588	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7545910	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9700904	0.82[EUR][1000 genomes]
rs989423	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]

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	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
2	esv1794782	chr1:174900761-174925112	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9804056	SLC9A11	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174874000-174910000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:174874200-174938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:174876800-174933600	Weak transcription	Aorta	Aorta
4	chr1:174886000-174907200	Weak transcription	Primary T cells from cord blood	blood
5	chr1:174886400-174911600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr1:174889600-174907400	Weak transcription	Primary B cells from cord blood	blood
7	chr1:174891800-174908600	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:174893400-174907600	Weak transcription	GM12878-XiMat	blood
9	chr1:174897400-174910000	Weak transcription	Gastric	stomach
10	chr1:174897800-174907200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:174898800-174910600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:174899800-174915200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:174900800-174907600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr1:174900800-174907600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr1:174900800-174911000	Weak transcription	Brain Angular Gyrus	brain
16	chr1:174901000-174907800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr1:174901000-174909400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:174901000-174922200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr1:174901400-174907600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:174901600-174907200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr1:174901600-174907200	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:174901600-174907400	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr1:174901800-174908000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:174902200-174909000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr1:174902600-174907600	Weak transcription	Brain Cingulate Gyrus	brain
26	chr1:174902600-174908400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr1:174903800-174911000	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:174904400-174907200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr1:174904600-174907600	Weak transcription	Fetal Stomach	stomach
30	chr1:174904800-174907600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr1:174905400-174907200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr1:174905600-174907200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr1:174905600-174907200	Weak transcription	Fetal Intestine Large	intestine
34	chr1:174905800-174907200	Weak transcription	Fetal Intestine Small	intestine
35	chr1:174905800-174907800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:174905800-174910000	Weak transcription	Pancreas	Pancrea
37	chr1:174905800-174910600	Weak transcription	HepG2	liver
38	chr1:174905800-174911600	Weak transcription	Primary B cells from peripheral blood	blood
39	chr1:174907000-174907200	Enhancers	Primary monocytes fromperipheralblood	blood
40	chr1:174907000-174907200	Enhancers	Primary T cells fromperipheralblood	blood
41	chr1:174907000-174907200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr1:174907000-174907200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:174907000-174907200	Enhancers	Dnd41	blood
44	chr1:174907000-174908600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood

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