Variant report

Variant	rs61839847
Chromosome Location	chr1:246671855-246671856
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BATF	chr1:246671669-246671904	GM12878	blood:	n/a	n/a
2	HNF4A	chr1:246671679-246671918	HepG2	liver:	n/a	n/a
3	FOXA1	chr1:246671707-246671909	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:246671783..246672632-chr1:246690944..246691587,2	MCF-7	breast:

Variant related genes	Relation type
SMYD3	TF binding region

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs11802785	1.00[ASN][1000 genomes]
rs12046729	1.00[ASN][1000 genomes]
rs14373	1.00[ASN][1000 genomes]
rs3120697	1.00[ASN][1000 genomes]
rs3120698	1.00[ASN][1000 genomes]
rs3120699	1.00[ASN][1000 genomes]
rs3120700	1.00[ASN][1000 genomes]
rs3120701	1.00[ASN][1000 genomes]
rs3120702	1.00[ASN][1000 genomes]
rs3124069	1.00[ASN][1000 genomes]
rs3124107	1.00[ASN][1000 genomes]
rs3124108	1.00[ASN][1000 genomes]
rs3124109	1.00[ASN][1000 genomes]
rs3124110	1.00[ASN][1000 genomes]
rs3124111	1.00[ASN][1000 genomes]
rs3124112	1.00[ASN][1000 genomes]
rs3124113	1.00[ASN][1000 genomes]
rs3124114	1.00[ASN][1000 genomes]
rs3124115	1.00[ASN][1000 genomes]
rs3124116	1.00[ASN][1000 genomes]
rs3124117	1.00[ASN][1000 genomes]
rs3124118	1.00[ASN][1000 genomes]
rs3124119	1.00[ASN][1000 genomes]
rs3124120	1.00[ASN][1000 genomes]
rs3124122	1.00[ASN][1000 genomes]
rs3124124	1.00[ASN][1000 genomes]
rs3124127	1.00[ASN][1000 genomes]
rs3124128	1.00[ASN][1000 genomes]
rs3129566	1.00[ASN][1000 genomes]
rs3129567	1.00[ASN][1000 genomes]
rs3129568	1.00[ASN][1000 genomes]
rs3129571	1.00[ASN][1000 genomes]
rs3129572	1.00[ASN][1000 genomes]
rs3129576	1.00[ASN][1000 genomes]
rs3129585	1.00[ASN][1000 genomes]
rs35558093	1.00[ASN][1000 genomes]
rs4654255	1.00[ASN][1000 genomes]
rs4654256	1.00[ASN][1000 genomes]
rs4654257	1.00[ASN][1000 genomes]
rs4654258	1.00[ASN][1000 genomes]
rs4654259	1.00[ASN][1000 genomes]
rs4654260	1.00[ASN][1000 genomes]
rs4654271	1.00[ASN][1000 genomes]
rs4654272	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4654273	0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4654274	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4654289	1.00[ASN][1000 genomes]
rs61839802	1.00[ASN][1000 genomes]
rs61839803	1.00[ASN][1000 genomes]
rs61839819	1.00[ASN][1000 genomes]
rs61839829	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839830	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839841	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61839844	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs61839846	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61839849	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61839853	1.00[ASN][1000 genomes]
rs6661340	1.00[ASN][1000 genomes]
rs6696917	1.00[ASN][1000 genomes]
rs6700001	1.00[ASN][1000 genomes]
rs67600458	1.00[ASN][1000 genomes]
rs72760817	1.00[ASN][1000 genomes]
rs72760824	1.00[ASN][1000 genomes]
rs72760831	1.00[ASN][1000 genomes]
rs72778126	1.00[ASN][1000 genomes]
rs7517472	1.00[ASN][1000 genomes]
rs7517536	1.00[ASN][1000 genomes]
rs7526671	1.00[ASN][1000 genomes]
rs7527607	1.00[ASN][1000 genomes]
rs7531213	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7537146	1.00[ASN][1000 genomes]
rs764243	1.00[ASN][1000 genomes]
rs946004	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:36 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004119	chr1:245957145-246813150	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
2	nsv535389	chr1:245957145-246813150	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1014529	chr1:245957145-246817877	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1000654	chr1:245966390-246778182	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv535392	chr1:245966390-246778182	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv868852	chr1:245969229-246811220	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv948348	chr1:246090818-246853200	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv430402	chr1:246124959-246787448	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv497890	chr1:246143172-246778453	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv998930	chr1:246166737-246702012	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription 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	15 gene(s)	inside rSNPs	diseases
11	nsv1005825	chr1:246174208-246688635	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
12	nsv535398	chr1:246194546-246686301	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv1001462	chr1:246194546-246686358	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
14	nsv535399	chr1:246194546-246686358	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv949329	chr1:246220147-246710091	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS 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	15 gene(s)	inside rSNPs	diseases
16	nsv468839	chr1:246303128-246708467	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv549528	chr1:246303128-246708467	Weak transcription Enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
18	nsv1005573	chr1:246378676-246740427	Strong transcription Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
19	nsv535405	chr1:246378676-246740427	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
20	nsv549531	chr1:246406762-246681116	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
21	esv2757779	chr1:246407146-246740944	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats 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	17 gene(s)	inside rSNPs	diseases
22	esv2759012	chr1:246407146-246740944	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
23	nsv428346	chr1:246407146-246740944	Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
24	nsv1013800	chr1:246472691-246840960	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
25	nsv535409	chr1:246472691-246840960	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
26	nsv997661	chr1:246482924-246702012	Strong transcription Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
27	esv2762191	chr1:246546436-246815064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
28	nsv1006777	chr1:246585396-246702012	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
29	nsv535412	chr1:246585396-246702012	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
30	nsv1002805	chr1:246608164-246890518	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
31	nsv535413	chr1:246608164-246890518	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
32	nsv1010453	chr1:246645797-246815052	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
33	nsv998579	chr1:246666041-246817877	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
34	esv1822854	chr1:246668544-246685307	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
35	nsv522303	chr1:246668544-246692992	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
36	nsv525447	chr1:246668544-246698653	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:246671000-246672200	Enhancers	HepG2	liver
2	chr1:246671200-246672200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr1:246671200-246675000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr1:246671200-246676000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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