Variant report

Variant	rs9859279
Chromosome Location	chr3:195064898-195064899
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 154 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:135)

rs_ID	r²[population]
rs10439946	0.92[EUR][1000 genomes]
rs10439947	0.92[EUR][1000 genomes]
rs10439948	0.92[EUR][1000 genomes]
rs10439949	0.92[EUR][1000 genomes]
rs11706218	0.91[EUR][1000 genomes]
rs11718226	0.86[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12054139	0.91[EUR][1000 genomes]
rs12054333	0.89[EUR][1000 genomes]
rs12054406	0.89[EUR][1000 genomes]
rs12629884	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12630009	0.89[EUR][1000 genomes]
rs12636736	0.93[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13316914	0.85[EUR][1000 genomes]
rs13317705	0.92[EUR][1000 genomes]
rs13317782	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13320698	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13325966	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1353133	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1538768	0.92[EUR][1000 genomes]
rs1826584	0.89[EUR][1000 genomes]
rs1890853	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1994880	0.89[EUR][1000 genomes]
rs1994881	0.89[EUR][1000 genomes]
rs2000052	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2029708	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2050806	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2066154	0.89[EUR][1000 genomes]
rs2131685	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2275518	0.89[EUR][1000 genomes]
rs2410792	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4677668	0.89[EUR][1000 genomes]
rs4677669	0.91[EUR][1000 genomes]
rs4677826	0.91[EUR][1000 genomes]
rs4677827	0.91[EUR][1000 genomes]
rs4677828	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4677829	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs4677832	0.92[EUR][1000 genomes]
rs4677833	0.91[EUR][1000 genomes]
rs4677837	0.89[EUR][1000 genomes]
rs4677838	0.89[EUR][1000 genomes]
rs4677839	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4677840	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4677842	0.89[EUR][1000 genomes]
rs4677843	0.89[EUR][1000 genomes]
rs4677844	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57760978	0.91[EUR][1000 genomes]
rs58067895	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58178384	0.89[EUR][1000 genomes]
rs59004692	0.85[EUR][1000 genomes]
rs59551685	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60100329	0.91[EUR][1000 genomes]
rs60177727	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs62287069	0.89[EUR][1000 genomes]
rs62287106	0.89[EUR][1000 genomes]
rs62287107	0.91[EUR][1000 genomes]
rs62287108	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs62287109	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62287111	0.92[EUR][1000 genomes]
rs62287119	0.91[EUR][1000 genomes]
rs62288360	0.92[EUR][1000 genomes]
rs62288364	0.89[EUR][1000 genomes]
rs62288365	0.89[EUR][1000 genomes]
rs62288367	0.89[EUR][1000 genomes]
rs62288369	0.89[EUR][1000 genomes]
rs62288441	0.85[EUR][1000 genomes]
rs62288442	0.83[EUR][1000 genomes]
rs6437373	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs6437375	0.92[EUR][1000 genomes]
rs6437376	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6437471	0.91[EUR][1000 genomes]
rs6763335	0.91[EUR][1000 genomes]
rs6763588	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6771771	0.92[EUR][1000 genomes]
rs6778652	0.85[EUR][1000 genomes]
rs6781311	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6785382	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6788868	0.85[EUR][1000 genomes]
rs6791563	0.85[EUR][1000 genomes]
rs6794216	0.90[EUR][1000 genomes]
rs6800221	0.83[EUR][1000 genomes]
rs6800562	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6801007	0.89[EUR][1000 genomes]
rs6801315	0.92[EUR][1000 genomes]
rs6801750	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6803477	0.82[EUR][1000 genomes]
rs6803763	0.91[EUR][1000 genomes]
rs6806763	0.81[EUR][1000 genomes]
rs6806850	0.91[EUR][1000 genomes]
rs716898	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73208931	0.83[EUR][1000 genomes]
rs7430205	0.91[EUR][1000 genomes]
rs7611090	0.86[EUR][1000 genomes]
rs7616598	0.89[EUR][1000 genomes]
rs7617936	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7618499	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7621133	0.89[EUR][1000 genomes]
rs7623135	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7627054	0.91[EUR][1000 genomes]
rs7627671	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7635603	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7635906	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7636824	0.89[EUR][1000 genomes]
rs7639146	0.91[EUR][1000 genomes]
rs7641810	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs7650623	0.92[EUR][1000 genomes]
rs7652612	0.87[EUR][1000 genomes]
rs7653406	0.89[EUR][1000 genomes]
rs9288744	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9288746	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9681021	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9809730	0.92[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9812506	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9813425	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9814214	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9814344	0.89[EUR][1000 genomes]
rs9817672	0.89[EUR][1000 genomes]
rs9821765	0.85[EUR][1000 genomes]
rs9826999	0.89[EUR][1000 genomes]
rs9836665	0.89[EUR][1000 genomes]
rs9844354	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9846555	0.89[EUR][1000 genomes]
rs9847544	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9848201	0.92[EUR][1000 genomes]
rs9848473	0.89[EUR][1000 genomes]
rs9854941	0.91[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9855453	0.94[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9859902	0.94[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs9860798	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9862710	0.91[EUR][1000 genomes]
rs9864603	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9866537	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9868768	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9870236	0.89[EUR][1000 genomes]
rs9876967	0.83[EUR][1000 genomes]
rs9879305	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
2	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
3	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
4	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
5	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
9	esv1832781	chr3:194902818-195528226	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
10	nsv432508	chr3:194916131-195478861	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
11	nsv432510	chr3:194935314-195478861	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	59 gene(s)	inside rSNPs	diseases
12	nsv1005519	chr3:194964301-195340515	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
13	nsv432511	chr3:194986167-195479748	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
14	nsv432512	chr3:195007260-195475989	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
15	nsv526569	chr3:195038287-195123495	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
16	nsv878138	chr3:195057001-195477791	Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
17	nsv878139	chr3:195058837-195158031	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
18	esv1799680	chr3:195060129-195154361	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a
19	nsv878140	chr3:195062395-195096625	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9859279	XXYLT1	cis	Esophagus Mucosa	GTEx
rs9859279	XXYLT1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194992600-195090000	Weak transcription	Aorta	Aorta
2	chr3:194993000-195076000	Weak transcription	Fetal Heart	heart
3	chr3:195004000-195066600	Weak transcription	Small Intestine	intestine
4	chr3:195010000-195076400	Weak transcription	Brain Angular Gyrus	brain
5	chr3:195022600-195073400	Weak transcription	HMEC	breast
6	chr3:195022800-195073400	Weak transcription	NHEK	skin
7	chr3:195034800-195076800	Weak transcription	Psoas Muscle	Psoas
8	chr3:195040400-195066000	Strong transcription	Primary neutrophils fromperipheralblood	blood
9	chr3:195040400-195076400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:195040400-195076600	Weak transcription	Brain Anterior Caudate	brain
11	chr3:195040400-195079400	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr3:195040400-195108400	Weak transcription	Colonic Mucosa	Colon
13	chr3:195040600-195111200	Weak transcription	Fetal Brain Male	brain
14	chr3:195040800-195071200	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr3:195040800-195072800	Weak transcription	K562	blood
16	chr3:195040800-195073200	Weak transcription	Pancreas	Pancrea
17	chr3:195040800-195076400	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:195041000-195065400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr3:195041000-195066400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:195041000-195067200	Weak transcription	Brain Substantia Nigra	brain
21	chr3:195041000-195077000	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:195041000-195131200	Weak transcription	Gastric	stomach
23	chr3:195041200-195077200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr3:195041400-195076800	Weak transcription	Rectal Smooth Muscle	rectum
25	chr3:195041600-195071600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr3:195041600-195073600	Weak transcription	NHLF	lung
27	chr3:195041600-195077800	Weak transcription	Fetal Brain Female	brain
28	chr3:195045800-195065200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:195048800-195076800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr3:195049600-195106000	Weak transcription	HUVEC	blood vessel
31	chr3:195051800-195073800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr3:195051800-195077000	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:195052000-195071400	Weak transcription	HepG2	liver
34	chr3:195052000-195076400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr3:195052200-195070000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr3:195052200-195076200	Weak transcription	Colon Smooth Muscle	Colon
37	chr3:195052200-195076800	Weak transcription	Spleen	Spleen
38	chr3:195052200-195077000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:195052200-195102800	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr3:195052400-195073400	Weak transcription	HSMMtube	muscle
41	chr3:195052400-195076400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:195052400-195076800	Weak transcription	Ovary	ovary
43	chr3:195052400-195076800	Weak transcription	Right Ventricle	heart
44	chr3:195052400-195118000	Weak transcription	Stomach Smooth Muscle	stomach
45	chr3:195052600-195077200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:195052600-195090400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr3:195053800-195090200	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:195056000-195073600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr3:195057400-195066000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:195057800-195065200	Strong transcription	Primary T cells fromperipheralblood	blood

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