Variant report

Variant	rs9846976
Chromosome Location	chr3:53007995-53007996
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53004813..53006485-chr3:53007030..53009652,2	K562	blood:

Extended variants
information (count: 92 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs11130332	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1134546	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs11706243	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11707576	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11708223	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13072536	0.80[CEU][hapmap]
rs13082061	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13083728	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs1573815	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs17304995	1.00[CEU][hapmap];0.88[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs2245424	0.91[JPT][hapmap]
rs2246556	0.84[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2255107	0.82[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs2257216	0.91[JPT][hapmap]
rs2276817	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs2276825	0.94[CEU][hapmap];0.88[TSI][hapmap]
rs2336162	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs2336666	0.83[EUR][1000 genomes]
rs2336669	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2336670	0.90[JPT][hapmap]
rs2336671	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2564947	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2581779	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2581780	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2581796	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2581797	0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2581801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581802	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2581803	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs2581805	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2581810	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2581815	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2581820	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2581823	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2710314	0.91[JPT][hapmap]
rs2710342	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2710345	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34230854	0.89[EUR][1000 genomes]
rs35380116	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3733047	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs4302374	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs4519686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687554	0.82[CEU][hapmap];0.81[TSI][hapmap]
rs4687559	0.84[EUR][1000 genomes]
rs4687560	0.84[EUR][1000 genomes]
rs4687658	0.82[CEU][hapmap]
rs4687663	0.82[CEU][hapmap]
rs4687672	0.81[CEU][hapmap]
rs4687692	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687699	0.80[EUR][1000 genomes]
rs59989280	0.88[EUR][1000 genomes]
rs6445538	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs6445539	0.82[CEU][hapmap];0.85[TSI][hapmap]
rs6445547	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs6445550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6768844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6770957	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6771610	0.84[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6773040	0.84[EUR][1000 genomes]
rs6789219	0.88[EUR][1000 genomes]
rs6792578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6797399	0.82[EUR][1000 genomes]
rs6801235	0.81[ASN][1000 genomes]
rs6803519	0.82[CEU][hapmap];0.82[GIH][hapmap];0.85[TSI][hapmap]
rs6805298	0.88[EUR][1000 genomes]
rs71301803	0.89[EUR][1000 genomes]
rs71301807	0.90[EUR][1000 genomes]
rs7621939	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7637082	0.82[EUR][1000 genomes]
rs7644973	0.90[EUR][1000 genomes]
rs7648514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7652131	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9311485	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9682464	0.94[CEU][hapmap]
rs9812543	0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9813024	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9823697	0.91[JPT][hapmap]
rs9825679	0.90[ASN][1000 genomes]
rs9828491	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9831409	0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9839035	0.82[EUR][1000 genomes]
rs9842974	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9844736	1.00[CEU][hapmap];0.88[GIH][hapmap];0.95[TSI][hapmap];0.83[EUR][1000 genomes]
rs9847024	0.92[EUR][1000 genomes]
rs9865094	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9870898	1.00[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs9876403	0.94[CEU][hapmap];0.96[GIH][hapmap];0.93[TSI][hapmap];0.86[EUR][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	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	esv1818974	chr3:52966316-53096394	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv3823	chr3:53003659-53051063	Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2756989	chr3:53006055-53039455	Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	esv2759149	chr3:53006055-53039455	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs9846976	MUSTN1	cis	Artery Aorta	GTEx
rs9846976	ITIH4-AS1	cis	Artery Aorta	GTEx
rs9846976	GNL3	cis	cerebellum	SCAN
rs9846976	ITIH4	cis	parietal	SCAN
rs9846976	ITIH4-AS1	cis	lung	GTEx
rs9846976	TMEM110	cis	parietal	SCAN
rs9846976	ITIH4	cis	lymphoblastoid	seeQTL
rs9846976	ITIH4	cis	cerebellum	SCAN
rs9846976	SERBP1P3	cis	lung	GTEx
rs9846976	RFT1	cis	cerebellum	SCAN
rs9846976	RBM6	cis	cerebellum	SCAN
rs9846976	NT5DC2	cis	parietal	SCAN
rs9846976	GNL3	cis	parietal	SCAN
rs9846976	TMEM110	cis	cerebellum	SCAN
rs9846976	ITIH4-AS1	cis	Artery Tibial	GTEx
rs9846976	WDR6	cis	cerebellum	SCAN
rs9846976	AMT	cis	parietal	SCAN
rs9846976	SEMA3G	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52954000-53012200	Weak transcription	Esophagus	oesophagus
2	chr3:52954200-53012200	Weak transcription	Pancreas	Pancrea
3	chr3:52962400-53012400	Weak transcription	Adipose Nuclei	Adipose
4	chr3:52964600-53012200	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:52965000-53039800	Weak transcription	Left Ventricle	heart
6	chr3:52965600-53008200	Weak transcription	GM12878-XiMat	blood
7	chr3:52969000-53008000	Weak transcription	Colon Smooth Muscle	Colon
8	chr3:52975000-53008000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:52977600-53017000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:52986400-53012200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:52987200-53017400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:52987600-53009400	Weak transcription	Placenta	Placenta
13	chr3:52987600-53014200	Weak transcription	Fetal Thymus	thymus
14	chr3:52987600-53014200	Weak transcription	Thymus	Thymus
15	chr3:52987800-53017000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:52987800-53017000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr3:52988000-53014200	Weak transcription	Primary T cells from cord blood	blood
18	chr3:52992000-53015800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr3:52993800-53016800	Weak transcription	Primary B cells from cord blood	blood
20	chr3:52997200-53008200	Weak transcription	A549	lung
21	chr3:52999000-53008200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr3:53001400-53008000	Weak transcription	Osteobl	bone
23	chr3:53001800-53008800	Weak transcription	Brain Substantia Nigra	brain
24	chr3:53002000-53017600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr3:53002400-53012000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr3:53002400-53013400	Weak transcription	Liver	Liver
27	chr3:53003400-53016000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:53003400-53017000	Weak transcription	Dnd41	blood
29	chr3:53004000-53012200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:53004200-53014800	Weak transcription	Fetal Intestine Small	intestine
31	chr3:53006000-53008200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr3:53006200-53015600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:53006400-53008000	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr3:53006400-53012000	Weak transcription	Fetal Heart	heart
35	chr3:53007800-53008400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr3:53007800-53008400	Enhancers	Hela-S3	cervix
37	chr3:53007800-53008600	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr3:53007800-53008600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--

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