Variant report

Variant	rs10489759
Chromosome Location	chr1:189589339-189589340
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:189588020..189590795-chr1:189591484..189594244,3	MCF-7	breast:
2	chr1:189589226..189590045-chr1:189662088..189662866,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10489757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10922224	1.00[ASN][1000 genomes]
rs12239274	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13373810	1.00[ASN][1000 genomes]
rs13374026	1.00[ASN][1000 genomes]
rs13374345	1.00[ASN][1000 genomes]
rs13374475	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs13374577	1.00[ASN][1000 genomes]
rs13376653	1.00[ASN][1000 genomes]
rs1502596	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs155905	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs155906	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs155907	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16829235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16829236	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830926	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16830947	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16830955	1.00[ASN][1000 genomes]
rs16830959	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16830968	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16830981	1.00[ASN][1000 genomes]
rs17838226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs269736	1.00[ASN][1000 genomes]
rs28488254	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28702743	1.00[ASN][1000 genomes]
rs28849150	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs28862285	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs41320655	1.00[ASN][1000 genomes]
rs475778	0.91[EUR][1000 genomes]
rs545601	0.91[EUR][1000 genomes]
rs55745910	1.00[ASN][1000 genomes]
rs55841697	1.00[ASN][1000 genomes]
rs56360155	1.00[ASN][1000 genomes]
rs56366121	0.96[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57315806	1.00[ASN][1000 genomes]
rs57343173	1.00[ASN][1000 genomes]
rs57523607	0.92[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs57779265	1.00[ASN][1000 genomes]
rs58571092	1.00[ASN][1000 genomes]
rs59734914	1.00[ASN][1000 genomes]
rs61105636	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662467	1.00[ASN][1000 genomes]
rs73049532	1.00[ASN][1000 genomes]
rs73049547	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs73049572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74138324	1.00[ASN][1000 genomes]
rs74138330	1.00[ASN][1000 genomes]
rs74138441	1.00[ASN][1000 genomes]
rs74138445	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7537185	1.00[ASN][1000 genomes]
rs9725923	0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:42 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv548483	chr1:188802542-189672228	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv1009962	chr1:188849003-189605507	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv535232	chr1:188849003-189605507	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv999435	chr1:188997868-189849121	Weak transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1012877	chr1:189035500-189804333	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv872658	chr1:189069537-189675416	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv534452	chr1:189129332-189924389	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv872662	chr1:189211622-189741561	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv872673	chr1:189238665-189731048	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv2757763	chr1:189246533-189649328	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	esv2758982	chr1:189246533-189649328	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv872683	chr1:189286816-189748851	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
13	nsv1014923	chr1:189305229-189614654	Enhancers Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv872696	chr1:189321018-189620278	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv523001	chr1:189350700-189600151	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv427863	chr1:189356268-189709137	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
17	nsv548516	chr1:189418504-189589339	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
18	nsv548517	chr1:189427759-189589339	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
19	nsv548518	chr1:189428501-189589339	Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
20	nsv1012568	chr1:189429394-189594302	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
21	nsv1003741	chr1:189447275-189702125	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
22	nsv535241	chr1:189447275-189702125	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
23	nsv1010463	chr1:189488465-189612966	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
24	nsv1005794	chr1:189488465-190063923	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
25	nsv872709	chr1:189512884-189600151	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
26	nsv872710	chr1:189512884-189695297	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
27	nsv1004742	chr1:189526599-189652035	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
28	nsv872711	chr1:189528943-189620278	Active TSS Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
29	nsv872712	chr1:189528943-189731048	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
30	nsv872713	chr1:189543576-189620278	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region	n/a	inside rSNPs	diseases
31	nsv872714	chr1:189543576-189636292	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
32	nsv872715	chr1:189543576-189731048	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
33	nsv466628	chr1:189548411-189600151	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
34	nsv548522	chr1:189548411-189600151	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
35	nsv1009290	chr1:189554045-189908459	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
36	nsv497885	chr1:189562225-190086077	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
37	nsv872716	chr1:189568547-189736833	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
38	nsv1011437	chr1:189579890-189642442	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
39	nsv872717	chr1:189585380-189748851	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
40	nsv947458	chr1:189588116-189591869	Active TSS Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
41	esv18854	chr1:189589192-189589675	Enhancers Flanking Active TSS Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
42	nsv872718	chr1:189589339-189731048	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Immune response to smallpox vaccine (IL-6)	22542470	GWAS catalog

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:189588600-189589600	Enhancers	Muscle Satellite Cultured Cells	--
2	chr1:189588600-189589600	Enhancers	HUVEC	blood vessel
3	chr1:189588600-189589800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:189588800-189589400	Enhancers	NHEK	skin
5	chr1:189588800-189589800	Enhancers	HMEC	breast
6	chr1:189589000-189589400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr1:189589000-189589400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr1:189589000-189589400	Flanking Active TSS	A549	lung
9	chr1:189589000-189589400	Enhancers	Hela-S3	cervix
10	chr1:189589000-189589400	Enhancers	NH-A	brain
11	chr1:189589000-189589400	Enhancers	Osteobl	bone

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