Variant report

Variant	rs7538588
Chromosome Location	chr1:174874295-174874296
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174873499..174877029-chr1:174967125..174970302,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10436863	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1046439	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap]
rs11590474	1.00[LWK][hapmap]
rs12083837	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1653626	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];0.96[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs1653627	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]
rs1653632	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];0.96[MKK][hapmap];0.98[TSI][hapmap];0.86[EUR][1000 genomes]
rs170768	0.82[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap]
rs1754349	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1754351	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs1754355	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs1793297	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];0.84[EUR][1000 genomes]
rs1793300	0.82[EUR][1000 genomes]
rs1793309	0.88[EUR][1000 genomes]
rs1793319	0.82[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap]
rs1801791	0.86[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap]
rs1984418	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][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];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2285210	0.91[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap]
rs2981894	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2987869	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs2987874	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs3018410	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];0.96[MKK][hapmap];0.98[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3118980	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs3133270	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs332771	0.81[EUR][1000 genomes]
rs332773	0.80[EUR][1000 genomes]
rs332783	0.84[CEU][hapmap]
rs332789	0.81[EUR][1000 genomes]
rs332795	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap]
rs332796	0.82[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap]
rs333418	0.82[CEU][hapmap];0.85[GIH][hapmap];0.80[MEX][hapmap]
rs3753563	1.00[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.81[MKK][hapmap]
rs4233195	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs444678	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs461910	0.81[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];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55741955	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61828140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61828142	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6425305	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[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6425309	0.81[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];1.00[LWK][hapmap];0.86[MKK][hapmap]
rs6425310	0.91[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap]
rs6656665	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6658861	0.82[CEU][hapmap];0.85[GIH][hapmap];0.84[MEX][hapmap]
rs6665216	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];0.90[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6669560	0.91[CHB][hapmap];0.90[CHD][hapmap];1.00[LWK][hapmap]
rs66700013	0.80[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6688577	0.84[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap]
rs7355181	0.84[TSI][hapmap]
rs7545910	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9700904	0.82[EUR][1000 genomes]
rs9804056	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]
rs989423	1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7538588	SLC9A11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174844800-174874400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:174844800-174877400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:174847600-174874400	Weak transcription	Esophagus	oesophagus
4	chr1:174850200-174874800	Weak transcription	Fetal Stomach	stomach
5	chr1:174852800-174874800	Weak transcription	Spleen	Spleen
6	chr1:174856800-174876400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:174861400-174876200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:174861400-174902400	Weak transcription	Left Ventricle	heart
9	chr1:174862800-174882400	Weak transcription	Fetal Lung	lung
10	chr1:174863200-174883200	Weak transcription	Small Intestine	intestine
11	chr1:174863400-174881400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:174863800-174876000	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr1:174863800-174883000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:174864200-174882000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr1:174868800-174874800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr1:174869000-174875200	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr1:174869600-174874400	Weak transcription	Brain Hippocampus Middle	brain
18	chr1:174869600-174877600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:174869800-174874600	Weak transcription	Primary T cells from cord blood	blood
20	chr1:174870000-174874800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr1:174870000-174877600	Weak transcription	Brain Anterior Caudate	brain
22	chr1:174871800-174878400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:174871800-174882000	Strong transcription	HUES48 Cell Line	embryonic stem cell
24	chr1:174872000-174875600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:174872000-174885800	Weak transcription	Pancreas	Pancrea
26	chr1:174872000-174886000	Weak transcription	Gastric	stomach
27	chr1:174872000-174889200	Weak transcription	Primary B cells from cord blood	blood
28	chr1:174872200-174875200	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr1:174872200-174882600	Weak transcription	Stomach Mucosa	stomach
30	chr1:174872400-174888800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr1:174872800-174900400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr1:174873200-174874600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr1:174873200-174876800	ZNF genes & repeats	Fetal Intestine Small	intestine
34	chr1:174873400-174897200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr1:174873600-174875200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:174873600-174875400	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr1:174873600-174882000	Weak transcription	K562	blood
38	chr1:174873800-174875400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
39	chr1:174874000-174875600	ZNF genes & repeats	Fetal Intestine Large	intestine
40	chr1:174874000-174910000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr1:174874200-174874600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr1:174874200-174885400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:174874200-174885800	Weak transcription	Duodenum Mucosa	Duodenum
44	chr1:174874200-174938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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