Variant report

Variant	rs6718068
Chromosome Location	chr2:48604978-48604979
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	chr2:48604176..48606531-chr2:48606806..48608312,2	K562	blood:

Extended variants
information (count: 118 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs10153773	0.87[JPT][hapmap]
rs10169629	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10199431	0.87[JPT][hapmap]
rs10208627	0.86[ASN][1000 genomes]
rs10454133	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs10454134	0.83[JPT][hapmap]
rs10495951	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10495952	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11676168	0.91[JPT][hapmap]
rs11679523	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11680719	0.87[JPT][hapmap];0.92[EUR][1000 genomes]
rs11680916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11682044	0.83[JPT][hapmap]
rs11682633	0.92[ASN][1000 genomes]
rs11683099	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11683639	0.87[JPT][hapmap]
rs11685861	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11686007	0.86[ASN][1000 genomes]
rs11687708	0.81[ASN][1000 genomes]
rs11688481	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs11689622	0.87[JPT][hapmap]
rs11689645	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11690690	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11690748	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs11690845	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12052754	0.97[ASN][1000 genomes]
rs12105983	0.86[ASN][1000 genomes]
rs12328506	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13388291	0.86[JPT][hapmap]
rs13398791	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13401749	0.87[JPT][hapmap]
rs13432998	0.87[JPT][hapmap]
rs17037289	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17037298	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs17855177	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4316980	0.87[JPT][hapmap]
rs4344965	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.99[ASN][1000 genomes]
rs4411759	0.87[JPT][hapmap]
rs4438532	0.83[JPT][hapmap]
rs4547570	0.94[ASN][1000 genomes]
rs4606978	0.81[CHD][hapmap];0.83[JPT][hapmap]
rs4641990	0.91[JPT][hapmap]
rs4953572	0.95[CEU][hapmap];0.80[GIH][hapmap];0.94[TSI][hapmap];0.94[EUR][1000 genomes]
rs55660911	0.99[ASN][1000 genomes]
rs55744465	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55761545	0.90[ASN][1000 genomes]
rs55788229	0.81[ASN][1000 genomes]
rs56156294	0.92[ASN][1000 genomes]
rs56163539	0.88[ASN][1000 genomes]
rs56365822	0.83[ASN][1000 genomes]
rs56391806	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57131168	0.85[ASN][1000 genomes]
rs57537506	0.96[ASN][1000 genomes]
rs57893565	0.97[ASN][1000 genomes]
rs58012056	0.98[ASN][1000 genomes]
rs58978223	0.82[ASN][1000 genomes]
rs59045263	0.86[ASN][1000 genomes]
rs59697023	0.84[ASN][1000 genomes]
rs60042255	0.83[ASN][1000 genomes]
rs60815228	0.83[ASN][1000 genomes]
rs60825643	0.94[ASN][1000 genomes]
rs61303367	0.83[ASN][1000 genomes]
rs62137015	0.99[ASN][1000 genomes]
rs62137018	0.81[ASN][1000 genomes]
rs62137019	0.84[ASN][1000 genomes]
rs62137021	0.83[ASN][1000 genomes]
rs6545027	0.82[JPT][hapmap]
rs6545030	0.91[JPT][hapmap]
rs6545036	0.91[CHB][hapmap];0.98[CHD][hapmap];0.83[JPT][hapmap];0.82[MEX][hapmap];0.88[ASN][1000 genomes]
rs66705539	0.85[ASN][1000 genomes]
rs6705802	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6712029	0.91[JPT][hapmap]
rs6722246	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6735288	0.86[ASN][1000 genomes]
rs6743757	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6745580	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6747441	0.80[ASN][1000 genomes]
rs6749773	0.83[ASN][1000 genomes]
rs6756596	0.97[ASN][1000 genomes]
rs72818488	0.84[ASN][1000 genomes]
rs72818491	0.82[ASN][1000 genomes]
rs72818494	0.83[ASN][1000 genomes]
rs72818502	0.88[ASN][1000 genomes]
rs72820403	0.92[ASN][1000 genomes]
rs72820404	0.95[ASN][1000 genomes]
rs72820409	0.94[ASN][1000 genomes]
rs72820411	0.94[ASN][1000 genomes]
rs72820415	0.94[ASN][1000 genomes]
rs72820416	0.94[ASN][1000 genomes]
rs72820418	0.94[ASN][1000 genomes]
rs72820420	0.96[ASN][1000 genomes]
rs72820422	0.96[ASN][1000 genomes]
rs72820423	0.98[ASN][1000 genomes]
rs72820424	0.95[ASN][1000 genomes]
rs72820427	0.96[ASN][1000 genomes]
rs72820433	0.96[ASN][1000 genomes]
rs72820436	0.99[ASN][1000 genomes]
rs72820437	1.00[ASN][1000 genomes]
rs72820439	1.00[ASN][1000 genomes]
rs72820441	0.97[ASN][1000 genomes]
rs72820445	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72820454	0.83[ASN][1000 genomes]
rs7559431	0.92[ASN][1000 genomes]
rs7562069	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.84[YRI][hapmap];1.00[ASN][1000 genomes]
rs7562816	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7566239	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7568574	0.85[ASN][1000 genomes]
rs7573316	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7576964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7579932	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7600794	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7606104	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.96[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	nsv530831	chr2:48059709-48632317	Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv874001	chr2:48534363-48624007	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv874002	chr2:48547751-48610367	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
4	esv2762252	chr2:48554150-48741093	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv874003	chr2:48570509-48619869	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6718068	STON1-GTF2A1L	cis	cerebellum	SCAN
rs6718068	FBXO11	cis	cerebellum	SCAN
rs6718068	PPP1R21	cis	Thyroid	GTEx

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:48571200-48605200	Weak transcription	Colonic Mucosa	Colon
2	chr2:48581400-48608000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:48589400-48607400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:48590000-48607400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr2:48591600-48605000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:48592800-48605400	Strong transcription	HepG2	liver
7	chr2:48595200-48609200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:48595800-48605000	Weak transcription	Fetal Brain Male	brain
9	chr2:48597400-48608000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:48597800-48609400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr2:48598600-48607400	Weak transcription	Fetal Brain Female	brain
12	chr2:48598600-48609000	Weak transcription	Fetal Intestine Small	intestine
13	chr2:48598600-48612800	Weak transcription	Fetal Stomach	stomach
14	chr2:48598800-48605400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
15	chr2:48598800-48605400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr2:48599000-48605800	Strong transcription	Dnd41	blood
17	chr2:48599400-48608000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr2:48599600-48607800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr2:48599800-48606400	Strong transcription	HSMM	muscle
20	chr2:48599800-48607000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:48600000-48605200	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr2:48600000-48606000	Strong transcription	NHDF-Ad	bronchial
23	chr2:48600000-48607400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr2:48600000-48607400	Strong transcription	Primary T helper cells PMA-I stimulated	--
25	chr2:48600000-48608000	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr2:48600200-48605800	Strong transcription	Adipose Nuclei	Adipose
27	chr2:48600400-48605200	Strong transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:48600400-48605200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:48600400-48605600	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr2:48600400-48607200	Strong transcription	Primary B cells from peripheral blood	blood
31	chr2:48600400-48607400	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:48600400-48607400	Strong transcription	A549	lung
33	chr2:48600400-48607600	Strong transcription	GM12878-XiMat	blood
34	chr2:48600600-48605400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr2:48600600-48605800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr2:48600600-48605800	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr2:48600600-48607800	Strong transcription	Primary hematopoietic stem cells	blood
38	chr2:48600800-48605000	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:48600800-48605800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr2:48600800-48605800	Strong transcription	Fetal Thymus	thymus
41	chr2:48600800-48607200	Strong transcription	Placenta	Placenta
42	chr2:48600800-48607400	Strong transcription	Liver	Liver
43	chr2:48600800-48607600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr2:48601000-48605000	Strong transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:48601000-48605200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr2:48601000-48606600	Strong transcription	Primary B cells from cord blood	blood
47	chr2:48601000-48607000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr2:48601200-48605200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:48601400-48605200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
50	chr2:48602000-48605200	Strong transcription	Primary T killer naive cells fromperipheralblood	blood

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