Variant report

Variant	rs539340
Chromosome Location	chr1:144338703-144338704
allele	C/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	POLR2A	chr1:144338543-144342331	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:144338526-144342260	GM12892	blood:	n/a	n/a
3	POLR2A	chr1:144338565-144341398	GM12891	blood:	n/a	n/a
4	POU2F2	chr1:144338543-144342272	GM12878	blood:	n/a	chr1:144339813-144339825 chr1:144340359-144340371 chr1:144340330-144340342
5	FOXA1	chr1:144338410-144338814	HepG2	liver:	n/a	n/a
6	POU2F2	chr1:144338656-144338873	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:144337584-144342475	H1-hESC	embryonic stem cell:	n/a	n/a
8	GATA2	chr1:144338538-144339738	K562	blood:	n/a	chr1:144339268-144339276 chr1:144339530-144339540
9	POLR2A	chr1:144338555-144341464	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr1:144338465-144342306	GM12892	blood:	n/a	n/a
11	IRF4	chr1:144338617-144342258	GM12878	blood:	n/a	chr1:144339619-144339633
12	POLR2A	chr1:144338570-144342243	GM12891	blood:	n/a	n/a
13	PAX5	chr1:144338533-144342278	GM12878	blood:	n/a	n/a
14	IRF4	chr1:144338681-144342389	GM12878	blood:	n/a	chr1:144339619-144339633
15	POLR2A	chr1:144338422-144342304	GM12878	blood:	n/a	n/a
16	BATF	chr1:144338647-144338871	GM12878	blood:	n/a	n/a
17	USF1	chr1:144338676-144338806	HepG2	liver:	n/a	n/a
18	SP1	chr1:144337885-144341035	GM12878	blood:	n/a	chr1:144340474-144340487 chr1:144340334-144340343 chr1:144340327-144340336 chr1:144340341-144340355 chr1:144339395-144339404 chr1:144340335-144340349 chr1:144340443-144340452 chr1:144340442-144340456 chr1:144340330-144340344 chr1:144340442-144340452 chr1:144340327-144340337 chr1:144339394-144339408
19	BCL11A	chr1:144338573-144342305	GM12878	blood:	n/a	chr1:144341848-144341857 chr1:144341113-144341126 chr1:144340129-144340138 chr1:144341106-144341119 chr1:144339852-144339861 chr1:144340130-144340143 chr1:144341165-144341174 chr1:144340443-144340456 chr1:144342124-144342131
20	POLR2A	chr1:144338654-144342065	GM12891	blood:	n/a	n/a
21	POLR2A	chr1:144338593-144341420	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr1:144338556-144342328	GM12892	blood:	n/a	n/a
23	POLR2A	chr1:144338590-144342303	GM12892	blood:	n/a	n/a

Variant related genes	Relation type
LINC00623	TF binding region
ENSG00000231360	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:52 , 50 per page) page: 1 2

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1005946	chr1:144007818-144471989	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv1003583	chr1:144007818-144543442	Bivalent Enhancer Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	257 gene(s)	inside rSNPs	diseases
3	nsv1002681	chr1:144007818-144560590	Genic enhancers Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	257 gene(s)	inside rSNPs	diseases
4	nsv1012104	chr1:144007818-144682096	Weak transcription Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	260 gene(s)	inside rSNPs	diseases
5	nsv1006330	chr1:144007818-144849544	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	262 gene(s)	inside rSNPs	diseases
6	nsv1001989	chr1:144007818-144873327	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	265 gene(s)	inside rSNPs	diseases
7	nsv997949	chr1:144007818-144876884	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	265 gene(s)	inside rSNPs	diseases
8	nsv1010670	chr1:144007818-144880405	Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	265 gene(s)	inside rSNPs	diseases
9	nsv1010163	chr1:144007818-144884322	Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	265 gene(s)	inside rSNPs	diseases
10	nsv1014985	chr1:144007818-144949963	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
11	nsv1000552	chr1:144008574-144471989	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
12	nsv1002373	chr1:144013582-144682096	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	258 gene(s)	inside rSNPs	diseases
13	nsv1004765	chr1:144015838-144471989	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
14	nsv1007748	chr1:144015838-144682096	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	258 gene(s)	inside rSNPs	diseases
15	nsv997876	chr1:144033939-144538748	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
16	nsv524682	chr1:144034888-144617179	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	257 gene(s)	inside rSNPs	diseases
17	esv1823205	chr1:144036737-144471989	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
18	nsv1007246	chr1:144036737-144560590	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	255 gene(s)	inside rSNPs	diseases
19	nsv1006612	chr1:144050098-144560590	Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	254 gene(s)	inside rSNPs	diseases
20	esv1831165	chr1:144094693-144520821	Active TSS Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
21	esv1831653	chr1:144094693-144520821	Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
22	esv1828275	chr1:144274482-145098718	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
23	esv16808	chr1:144274528-144401707	Active TSS Enhancers	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv872204	chr1:144276537-144381335	Active TSS Enhancers	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
25	esv1816945	chr1:144300531-144520821	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
26	esv18861	chr1:144309226-144401707	Active TSS Enhancers	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
27	nsv946229	chr1:144311634-144375115	Active TSS Enhancers	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
28	nsv831281	chr1:144314723-144400447	Active TSS Enhancers	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
29	esv1851433	chr1:144318894-144518980	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
30	nsv872205	chr1:144320413-144520547	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
31	esv1828628	chr1:144320872-144399546	Active TSS Enhancers	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
32	esv1828066	chr1:144321072-144520821	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
33	esv1832004	chr1:144321072-144520821	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
34	esv1824612	chr1:144321072-144526927	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
35	nsv946735	chr1:144321218-144361447	Enhancers Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
36	esv1818814	chr1:144321594-144400814	Active TSS Enhancers	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
37	esv1848757	chr1:144321594-144400814	Active TSS Enhancers	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
38	esv1822627	chr1:144321686-144399449	Active TSS Enhancers	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
39	nsv7992	chr1:144321781-144453645	Active TSS Enhancers	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
40	esv2512286	chr1:144321887-144560360	Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	251 gene(s)	inside rSNPs	diseases
41	esv1848080	chr1:144322604-144400095	Active TSS Enhancers	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
42	esv1817555	chr1:144322604-144400814	Enhancers Active TSS	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
43	esv1843150	chr1:144322804-144520821	Active TSS Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
44	esv1842762	chr1:144322804-144526927	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
45	esv1850215	chr1:144328502-144399449	Active TSS Enhancers	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
46	esv1831113	chr1:144328502-144460455	Active TSS Enhancers	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
47	esv1830763	chr1:144331032-144399449	Active TSS	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
48	esv3333165	chr1:144337095-144340593	Active TSS	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases
49	esv1820451	chr1:144337333-144399449	Active TSS	TF binding region CpG island lncRNA	4 gene(s)	inside rSNPs	diseases
50	nsv1014641	chr1:144337917-144880405	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	259 gene(s)	inside rSNPs	diseases

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Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
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