Variant report

Variant	rs17389184
Chromosome Location	chr1:209916789-209916790
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr1:209916257-209916985	SK-N-SH	brain:	n/a	n/a
2	PBX3	chr1:209916401-209917066	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr1:209916209-209916951	U87	brain:	n/a	n/a
4	NFIC	chr1:209916299-209917074	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr1:209916235-209916931	U87	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000236136	TF binding region

Extended variants
information (count: 66 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1000282	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1000283	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10157973	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs10863783	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10863785	0.81[EUR][1000 genomes]
rs11119327	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11119328	0.80[MEX][hapmap]
rs11119330	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11119331	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11119332	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11119336	0.84[CEU][hapmap]
rs11119340	0.81[CHD][hapmap];0.93[MEX][hapmap]
rs11119341	1.00[MEX][hapmap]
rs11485195	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11487866	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11487867	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11807619	0.86[MEX][hapmap]
rs11808690	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12030655	0.81[EUR][1000 genomes]
rs12034758	0.89[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12059226	0.90[CEU][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12060420	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12060922	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12086634	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12090931	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12094117	0.90[CEU][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12116437	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12120361	0.90[CEU][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12138452	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1415542	0.90[CEU][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes]
rs17389198	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1999826	0.87[EUR][1000 genomes]
rs2236903	0.84[CEU][hapmap]
rs2272867	0.85[CEU][hapmap];0.81[CHD][hapmap];0.81[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes]
rs2282738	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs2282739	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs3765240	0.87[EUR][1000 genomes]
rs3766618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766619	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4844891	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs627670	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs6540549	0.81[CEU][hapmap]
rs6540550	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs6540551	0.81[EUR][1000 genomes]
rs6540553	0.85[CEU][hapmap]
rs6665715	0.85[CEU][hapmap];0.82[MEX][hapmap]
rs6672256	0.93[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs667681	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6679099	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6679405	0.85[CEU][hapmap]
rs6702301	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs6752	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7532324	0.81[EUR][1000 genomes]
rs7539852	0.90[CEU][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs7548781	0.85[CEU][hapmap];0.90[TSI][hapmap]
rs909710	0.85[CEU][hapmap];0.81[CHD][hapmap];0.93[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes]
rs932335	0.90[CEU][hapmap];0.81[EUR][1000 genomes]
rs9430012	0.90[CEU][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9430014	0.81[EUR][1000 genomes]
rs9430016	0.90[CEU][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.87[EUR][1000 genomes]
rs9430017	0.85[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999901	chr1:209600631-210205379	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1014034	chr1:209759648-210501731	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv873139	chr1:209828955-210050794	Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv1006632	chr1:209886202-209970355	Flanking Active TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
5	nsv1001588	chr1:209908876-209938243	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17389184	HSD11B1	cis	cerebellum	SCAN
rs17389184	SYT14	cis	parietal	SCAN
rs17389184	SRGAP2	cis	parietal	SCAN
rs17389184	IRF6	cis	cerebellum	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:209907600-209920800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:209914000-209917200	Enhancers	Liver	Liver
3	chr1:209914200-209916800	Enhancers	Fetal Intestine Large	intestine
4	chr1:209914200-209916800	Enhancers	Left Ventricle	heart
5	chr1:209914600-209917000	Enhancers	Ovary	ovary
6	chr1:209914800-209917800	Enhancers	Pancreas	Pancrea
7	chr1:209914800-209917800	Enhancers	Right Atrium	heart
8	chr1:209915200-209916800	Enhancers	Fetal Stomach	stomach
9	chr1:209915200-209916800	Enhancers	Gastric	stomach
10	chr1:209915200-209917200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:209915200-209920800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
12	chr1:209915200-209921000	Weak transcription	Spleen	Spleen
13	chr1:209915400-209917200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:209915400-209917600	Weak transcription	Lung	lung
15	chr1:209915400-209918600	Enhancers	Brain Angular Gyrus	brain
16	chr1:209915400-209920400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr1:209915400-209920800	Weak transcription	Esophagus	oesophagus
18	chr1:209915600-209920600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr1:209915800-209916800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:209915800-209917000	Enhancers	HMEC	breast
21	chr1:209915800-209917200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr1:209915800-209917200	Enhancers	Right Ventricle	heart
23	chr1:209915800-209917200	Enhancers	NH-A	brain
24	chr1:209915800-209919800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
25	chr1:209916000-209917000	Enhancers	Brain Anterior Caudate	brain
26	chr1:209916000-209920800	Weak transcription	Rectal Mucosa Donor 29	rectum
27	chr1:209916000-209920800	Weak transcription	GM12878-XiMat	blood
28	chr1:209916200-209916800	Enhancers	Duodenum Mucosa	Duodenum
29	chr1:209916200-209916800	Enhancers	Fetal Lung	lung
30	chr1:209916200-209917200	Enhancers	NHLF	lung
31	chr1:209916200-209917400	Enhancers	Brain Hippocampus Middle	brain
32	chr1:209916200-209917800	Enhancers	Fetal Heart	heart
33	chr1:209916200-209919800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:209916200-209920200	Weak transcription	Adipose Nuclei	Adipose
35	chr1:209916400-209916800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:209916400-209916800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:209916400-209916800	Weak transcription	Colon Smooth Muscle	Colon
38	chr1:209916400-209917200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr1:209916400-209917200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr1:209916400-209917200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr1:209916400-209917200	Enhancers	Osteobl	bone
42	chr1:209916400-209917400	Enhancers	Brain Cingulate Gyrus	brain
43	chr1:209916400-209918400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr1:209916400-209918800	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr1:209916600-209917000	Enhancers	Stomach Smooth Muscle	stomach
46	chr1:209916600-209917200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr1:209916600-209918800	Enhancers	Brain Substantia Nigra	brain
48	chr1:209916600-209919800	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links