Variant report

Variant	rs13401945
Chromosome Location	chr2:173488679-173488680
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PDK1-1	chr2:173488299-173488880	NONHSAT075516

Extended variants
information (count: 104 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10048692	0.80[ASN][1000 genomes]
rs10048707	0.80[ASN][1000 genomes]
rs10048825	0.80[ASN][1000 genomes]
rs10176813	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10178654	1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10180021	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10186869	0.80[ASN][1000 genomes]
rs10197678	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10199472	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10201129	0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10202550	0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10207262	1.00[ASN][1000 genomes]
rs10208151	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10210546	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10427189	0.80[ASN][1000 genomes]
rs10427315	0.80[ASN][1000 genomes]
rs10930562	0.80[TSI][hapmap]
rs11887454	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11890159	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11891127	0.80[ASN][1000 genomes]
rs11896032	0.80[ASN][1000 genomes]
rs11896178	0.80[ASN][1000 genomes]
rs11897165	0.80[ASN][1000 genomes]
rs11897495	0.80[ASN][1000 genomes]
rs11897582	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11898137	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11898565	1.00[JPT][hapmap]
rs11898890	0.80[ASN][1000 genomes]
rs11901110	0.80[ASN][1000 genomes]
rs11902810	0.80[ASN][1000 genomes]
rs11902907	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11904366	0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs12693005	0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12693007	0.80[ASN][1000 genomes]
rs12990751	0.80[ASN][1000 genomes]
rs13007707	1.00[JPT][hapmap]
rs13009291	0.80[ASN][1000 genomes]
rs13010205	0.80[ASN][1000 genomes]
rs13021042	0.80[CEU][hapmap]
rs13023751	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13024218	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13024431	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032610	0.80[ASN][1000 genomes]
rs13032692	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13385403	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs13385644	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13386103	0.80[ASN][1000 genomes]
rs13388338	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13392808	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13394924	0.83[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13401980	0.80[ASN][1000 genomes]
rs13405998	1.00[ASN][1000 genomes]
rs13408780	1.00[ASN][1000 genomes]
rs13415156	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13415174	0.80[ASN][1000 genomes]
rs13417334	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs13425344	1.00[ASN][1000 genomes]
rs1531151	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16860696	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs16860697	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs17299956	1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17702263	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs1869922	0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1982410	0.80[ASN][1000 genomes]
rs2290564	0.80[ASN][1000 genomes]
rs2599267	1.00[ASN][1000 genomes]
rs2606069	1.00[ASN][1000 genomes]
rs28537209	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3087500	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs34139806	0.80[ASN][1000 genomes]
rs34382224	0.96[EUR][1000 genomes]
rs34611798	1.00[ASN][1000 genomes]
rs34707897	0.80[ASN][1000 genomes]
rs34888332	0.80[ASN][1000 genomes]
rs35086707	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35156154	1.00[ASN][1000 genomes]
rs35665064	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35809888	0.80[ASN][1000 genomes]
rs35880823	0.80[ASN][1000 genomes]
rs35951155	0.80[ASN][1000 genomes]
rs35999155	0.82[EUR][1000 genomes]
rs36118221	0.80[ASN][1000 genomes]
rs3613	0.80[ASN][1000 genomes]
rs3769321	0.80[TSI][hapmap]
rs3816536	1.00[JPT][hapmap]
rs59104969	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62169270	0.80[ASN][1000 genomes]
rs62169301	1.00[ASN][1000 genomes]
rs66460331	0.80[ASN][1000 genomes]
rs6723872	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs6738196	0.80[TSI][hapmap]
rs6752257	0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.80[ASN][1000 genomes]
rs7566884	0.87[ASN][1000 genomes]
rs7567092	0.87[ASN][1000 genomes]
rs836589	1.00[ASN][1000 genomes]
rs9287957	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533927	chr2:173161637-173796894	Active TSS Enhancers Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv2760591	chr2:173396905-173719520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv875415	chr2:173444462-173501069	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv875416	chr2:173444462-173504674	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv583665	chr2:173460640-173643087	Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv875417	chr2:173460803-173501069	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv875418	chr2:173460803-173504674	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv3357213	chr2:173485406-173488804	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13401945	ZAK	cis	cerebellum	SCAN
rs13401945	LOC440925	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173454400-173489000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:173461400-173488800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:173461400-173504200	Weak transcription	NHEK	skin
4	chr2:173462200-173507400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:173463400-173489400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:173465600-173495200	Weak transcription	Ovary	ovary
7	chr2:173471800-173495600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:173472400-173488800	Weak transcription	Fetal Thymus	thymus
9	chr2:173472600-173504600	Weak transcription	Adipose Nuclei	Adipose
10	chr2:173474400-173489800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:173474600-173504400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:173478800-173496800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:173479600-173488800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr2:173479600-173489600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:173479600-173490200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr2:173479600-173495800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr2:173479600-173496200	Weak transcription	Thymus	Thymus
18	chr2:173479800-173494600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:173479800-173496000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr2:173480000-173488800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
21	chr2:173480000-173492200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr2:173480000-173493800	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:173480000-173494200	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr2:173480000-173495000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr2:173480000-173495200	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr2:173480000-173496000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:173480200-173495800	Weak transcription	GM12878-XiMat	blood
28	chr2:173480200-173499200	Weak transcription	HepG2	liver
29	chr2:173485800-173497200	Weak transcription	Brain Hippocampus Middle	brain
30	chr2:173487600-173488800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:173487800-173488800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr2:173487800-173489200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr2:173487800-173489200	Enhancers	NHDF-Ad	bronchial
34	chr2:173487800-173490000	Strong transcription	Dnd41	blood
35	chr2:173488000-173488800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:173488000-173489200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:173488000-173489400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr2:173488000-173489400	Strong transcription	Primary T cells from cord blood	blood
39	chr2:173488000-173489400	Enhancers	Duodenum Mucosa	Duodenum
40	chr2:173488000-173490000	Enhancers	Osteobl	bone
41	chr2:173488000-173490200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
42	chr2:173488200-173488800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
43	chr2:173488200-173488800	Weak transcription	Fetal Stomach	stomach
44	chr2:173488200-173489000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr2:173488200-173489000	Weak transcription	Fetal Muscle Leg	muscle
46	chr2:173488400-173489800	Weak transcription	HSMMtube	muscle
47	chr2:173488600-173488800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr2:173488600-173488800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:173488600-173488800	Weak transcription	NHLF	lung
50	chr2:173488600-173489200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell

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