Variant report

Variant	rs12037211
Chromosome Location	chr1:169218924-169218925
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 107 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10158131	0.86[MEX][hapmap]
rs10158265	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158861	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10800439	0.86[CHB][hapmap]
rs10800441	0.86[CHB][hapmap]
rs10919088	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10919102	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919140	0.81[CEU][hapmap];0.86[MEX][hapmap]
rs10919146	0.97[ASN][1000 genomes]
rs11800843	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap]
rs11808274	0.81[ASW][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs11809378	0.87[ASN][1000 genomes]
rs12023291	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12024897	0.86[CHB][hapmap]
rs12025233	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026996	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12029853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12030320	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12032783	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12033078	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12033253	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12035804	0.82[ASN][1000 genomes]
rs12036968	0.91[YRI][hapmap]
rs12038609	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12039443	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12040813	0.82[ASN][1000 genomes]
rs12043489	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12043545	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12045202	0.93[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12046139	0.82[CHB][hapmap];0.88[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12047231	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1400838	0.86[CEU][hapmap];0.89[JPT][hapmap]
rs1415928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1589113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs16828170	0.81[ASW][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs16862172	0.90[ASW][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.84[YRI][hapmap]
rs1980198	0.86[CHB][hapmap]
rs2235195	0.90[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.84[YRI][hapmap]
rs2268048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2275299	0.86[CHB][hapmap]
rs34710865	0.88[ASN][1000 genomes]
rs3766058	0.83[EUR][1000 genomes]
rs3766089	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3818844	0.86[CHB][hapmap]
rs3820058	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656670	0.86[CHB][hapmap]
rs56341747	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58585501	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs61806986	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61808865	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61808901	0.82[ASN][1000 genomes]
rs61808903	0.81[ASN][1000 genomes]
rs61808914	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61808915	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6664272	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6669741	0.85[CHB][hapmap]
rs6677410	0.86[CHB][hapmap]
rs6685556	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696810	0.86[CHB][hapmap]
rs6698149	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7521338	1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7534737	0.86[CHB][hapmap]
rs7539415	0.86[CHB][hapmap]
rs9633334	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9804101	0.92[CEU][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9988595	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9988604	1.00[ASW][hapmap];0.93[CEU][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:40 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	56 gene(s)	inside rSNPs	diseases
4	nsv429913	chr1:169177019-169296744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1834321	chr1:169180302-169240975	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv1845262	chr1:169180302-169240975	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv525520	chr1:169191860-169240084	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1845267	chr1:169191860-169240975	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv1849515	chr1:169191860-169240975	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv1012919	chr1:169200982-169324750	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
13	nsv1000254	chr1:169203554-169271792	Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	esv1792529	chr1:169207360-169241309	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
15	esv1796180	chr1:169207360-169241309	Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
16	esv1798593	chr1:169207360-169241309	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv1798636	chr1:169207360-169241309	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv1815887	chr1:169207360-169241309	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
19	esv1820986	chr1:169207360-169241309	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
20	esv1826976	chr1:169207360-169241309	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	esv1834829	chr1:169207360-169241309	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
22	esv1835188	chr1:169207360-169241309	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
23	esv1835323	chr1:169207360-169241309	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
24	esv1837297	chr1:169207360-169241309	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
25	esv1846574	chr1:169207360-169241309	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
26	esv1799599	chr1:169207360-169248783	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
27	esv1824460	chr1:169207360-169248783	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
28	esv1825991	chr1:169207360-169248783	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
29	esv1836551	chr1:169207360-169248783	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
30	esv1837116	chr1:169207360-169248783	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
31	esv1847716	chr1:169207360-169248783	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
32	esv1847725	chr1:169207360-169248783	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
33	nsv1009170	chr1:169207940-169270995	Weak transcription ZNF genes & repeats Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
34	esv1804244	chr1:169213979-169255892	Weak transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
35	esv1808551	chr1:169214647-169241274	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
36	esv1809993	chr1:169214651-169240812	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
37	esv1007713	chr1:169214801-169253471	Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
38	nsv508637	chr1:169214920-169268078	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
39	esv1810150	chr1:169215695-169240812	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
40	nsv947448	chr1:169216666-169239767	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12037211	C1orf114	cis	parietal	SCAN
rs12037211	FMO9P	cis	parietal	SCAN
rs12037211	C1orf114	cis	cerebellum	SCAN
rs12037211	SCYL3	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169172600-169227000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:169215200-169219000	Weak transcription	A549	lung
3	chr1:169216200-169219600	Weak transcription	Liver	Liver
4	chr1:169218600-169220600	Enhancers	Hela-S3	cervix
5	chr1:169218800-169219200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
6	chr1:169218800-169219200	Enhancers	Primary hematopoietic stem cells short term culture	blood

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