Variant report

Variant	rs6688577
Chromosome Location	chr1:174884161-174884162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10465483	0.90[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap]
rs10489332	0.85[YRI][hapmap]
rs1653626	0.84[ASW][hapmap];0.81[CEU][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap]
rs1653627	0.81[CEU][hapmap];0.85[GIH][hapmap]
rs1653632	0.84[ASW][hapmap];0.81[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap]
rs16847730	0.85[YRI][hapmap]
rs170768	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs1754351	0.81[CEU][hapmap];0.85[GIH][hapmap]
rs1754355	0.81[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap]
rs1793291	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1793293	0.85[EUR][1000 genomes]
rs1793297	0.81[CEU][hapmap];0.83[GIH][hapmap]
rs1793319	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1894200	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2187562	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs2861106	0.85[YRI][hapmap]
rs2987869	0.81[CEU][hapmap];0.81[GIH][hapmap]
rs2987874	0.81[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap]
rs3018410	0.84[ASW][hapmap];0.81[CEU][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap]
rs3118980	0.84[CEU][hapmap];0.85[GIH][hapmap]
rs3133270	0.81[CEU][hapmap]
rs332783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs332795	0.81[CEU][hapmap];0.85[GIH][hapmap]
rs332796	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs332799	0.81[EUR][1000 genomes]
rs333418	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs41498747	1.00[YRI][hapmap]
rs4233195	0.81[CEU][hapmap];0.83[GIH][hapmap];0.83[MEX][hapmap]
rs4650666	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651238	0.84[ASW][hapmap];0.82[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap]
rs6425305	0.84[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap]
rs6658861	0.86[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6665216	0.84[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][hapmap]
rs6700434	0.85[YRI][hapmap]
rs7538588	0.84[ASW][hapmap];0.85[CEU][hapmap];0.85[GIH][hapmap];0.88[MEX][hapmap]
rs7538650	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs913685	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9804056	0.84[ASW][hapmap];0.85[CEU][hapmap];0.83[GIH][hapmap];0.88[MEX][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
rs6688577	GPR52	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174861400-174902400	Weak transcription	Left Ventricle	heart
2	chr1:174872000-174885800	Weak transcription	Pancreas	Pancrea
3	chr1:174872000-174886000	Weak transcription	Gastric	stomach
4	chr1:174872000-174889200	Weak transcription	Primary B cells from cord blood	blood
5	chr1:174872400-174888800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr1:174872800-174900400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:174873400-174897200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr1:174874000-174910000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:174874200-174885400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
10	chr1:174874200-174885800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr1:174874200-174938200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:174875400-174885400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:174876800-174933600	Weak transcription	Aorta	Aorta
14	chr1:174877200-174885600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr1:174879800-174885400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr1:174879800-174885400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr1:174880200-174885600	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr1:174881600-174884400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr1:174881600-174884400	Enhancers	Fetal Intestine Small	intestine
20	chr1:174881800-174885400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:174882000-174885000	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr1:174882000-174885400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:174882200-174885400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr1:174882200-174885600	Weak transcription	GM12878-XiMat	blood
25	chr1:174883000-174884200	Enhancers	Fetal Intestine Large	intestine
26	chr1:174883000-174885400	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr1:174883200-174884400	Enhancers	Fetal Kidney	kidney
28	chr1:174883400-174884800	Enhancers	Fetal Brain Male	brain
29	chr1:174883400-174885000	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr1:174883400-174885400	Weak transcription	Stomach Mucosa	stomach
31	chr1:174883600-174884400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr1:174883600-174885800	Weak transcription	Small Intestine	intestine
33	chr1:174883600-174889200	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr1:174883600-174900600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr1:174883800-174884400	Enhancers	Primary neutrophils fromperipheralblood	blood
36	chr1:174883800-174884400	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr1:174883800-174885400	Weak transcription	K562	blood
38	chr1:174883800-174889600	Weak transcription	Fetal Lung	lung
39	chr1:174884000-174885800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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