Variant report

Variant	rs10841753
Chromosome Location	chr12:21321370-21321371
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 80 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1000691	1.00[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.97[ASN][1000 genomes]
rs10444413	0.93[CEU][hapmap]
rs10770789	0.88[ASN][1000 genomes]
rs10841755	0.97[ASN][1000 genomes]
rs11045808	0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.92[ASN][1000 genomes]
rs11045813	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs11045814	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11045816	0.93[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs11045818	0.85[CEU][hapmap]
rs11045819	0.85[CEU][hapmap]
rs11045820	0.85[CEU][hapmap]
rs11045821	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs11045823	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs11045824	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs11045825	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs11045827	0.97[ASN][1000 genomes]
rs11045828	0.98[ASN][1000 genomes]
rs11045829	0.97[ASN][1000 genomes]
rs11045833	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11045834	1.00[CHB][hapmap];0.90[CHD][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs1120964	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12311454	1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.99[ASN][1000 genomes]
rs12313639	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12427008	0.83[CHB][hapmap]
rs12812279	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs12819994	0.80[EUR][1000 genomes]
rs12821068	0.80[EUR][1000 genomes]
rs12821228	0.80[EUR][1000 genomes]
rs17329885	0.85[CEU][hapmap]
rs2169968	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2219828	0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.92[ASN][1000 genomes]
rs2291074	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2417957	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2417967	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs4149037	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.98[ASN][1000 genomes]
rs4149041	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.93[YRI][hapmap];0.98[ASN][1000 genomes]
rs4149049	0.98[ASN][1000 genomes]
rs4149063	0.83[CHB][hapmap]
rs4149064	0.82[CHB][hapmap]
rs4149068	0.83[CHB][hapmap]
rs4149070	0.83[CHB][hapmap]
rs4149072	0.83[CHB][hapmap]
rs4381410	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs717958	0.83[CHB][hapmap]
rs7296796	0.89[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.92[ASN][1000 genomes]
rs7310315	0.93[ASN][1000 genomes]
rs7959887	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898872	chr12:21000586-21413632	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1045460	chr12:21007732-21348247	Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1048648	chr12:21007732-21410089	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv949142	chr12:21008498-21382619	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv948700	chr12:21008498-21422492	Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv531958	chr12:21008499-21377322	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1039633	chr12:21008519-21332904	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1047113	chr12:21008519-21402544	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv541411	chr12:21008519-21402544	ZNF genes & repeats Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
10	nsv515735	chr12:21010048-21420712	Enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv933139	chr12:21011077-21404166	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
12	nsv557710	chr12:21011480-21404832	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1038517	chr12:21017375-21356781	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv541412	chr12:21017375-21356781	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv1052893	chr12:21017376-21356782	Enhancers Strong transcription Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv541413	chr12:21017376-21356782	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
17	nsv1051005	chr12:21017575-21356642	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	nsv541414	chr12:21017575-21356642	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	nsv933316	chr12:21017576-21404166	ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	nsv916519	chr12:21017673-21356568	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv469159	chr12:21124371-21404832	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
22	nsv557717	chr12:21124371-21404832	Enhancers Strong transcription ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
23	nsv1052587	chr12:21149131-21420712	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
24	nsv1050396	chr12:21152478-21420712	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
25	nsv1054132	chr12:21165101-21402544	Enhancers Strong transcription Genic enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
26	nsv541415	chr12:21165101-21402544	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
27	nsv933284	chr12:21171894-21404166	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
28	esv3439156	chr12:21207396-21370189	Genic enhancers Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
29	nsv1041711	chr12:21236384-21402544	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
30	nsv1048033	chr12:21267568-21336958	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
31	nsv898880	chr12:21282953-21321482	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
32	nsv898882	chr12:21294293-21321482	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
33	nsv898883	chr12:21294293-21450917	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Methotrexate phramacokinetics (acute lymphoblastic leukemia)	19901119	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10841753	GOLT1B	cis	parietal	SCAN
rs10841753	LST-3TM12	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:21321000-21321400	Genic enhancers	Liver	Liver

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