Variant report

Variant	rs62354163
Chromosome Location	chr5:27473229-27473230
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:76)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:76 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr5:27473044-27473390	PANC-1	pancreas:	n/a	n/a
2	POLR2A	chr5:27473027-27473334	HepG2	liver:	n/a	n/a
3	POLR2A	chr5:27472073-27473434	HepG2	liver:	n/a	n/a
4	POLR2A	chr5:27473200-27473272	GM12878	blood:	n/a	n/a
5	MXI1	chr5:27473134-27473269	K562	blood:	n/a	n/a
6	POLR2A	chr5:27472136-27473435	GM12878	blood:	n/a	n/a
7	MYC	chr5:27473100-27473789	K562	blood:	n/a	n/a
8	TAF1	chr5:27473023-27473337	Hela-S3	cervix:	n/a	n/a
9	TAF1	chr5:27473003-27473365	H1-hESC	embryonic stem cell:	n/a	n/a
10	CEBPB	chr5:27472163-27473883	Hela-S3	cervix:	n/a	n/a
11	TAF1	chr5:27473016-27473336	Hela-S3	cervix:	n/a	n/a
12	POLR2A	chr5:27471986-27473289	HepG2	liver:	n/a	n/a
13	MAX	chr5:27472044-27474378	Hela-S3	cervix:	n/a	n/a
14	BRCA1	chr5:27472043-27473952	Hela-S3	cervix:	n/a	n/a
15	YY1	chr5:27473021-27473390	HepG2	liver:	n/a	chr5:27473203-27473215
16	MYBL2	chr5:27473084-27473691	HepG2	liver:	n/a	n/a
17	POLR2A	chr5:27473039-27473348	Hela-S3	cervix:	n/a	n/a
18	TBP	chr5:27471898-27474340	Hela-S3	cervix:	n/a	n/a
19	MAX	chr5:27472997-27473351	H1-hESC	embryonic stem cell:	n/a	n/a
20	HEY1	chr5:27473012-27473290	K562	blood:	n/a	n/a
21	YY1	chr5:27473044-27473346	GM12892	blood:	n/a	chr5:27473203-27473215
22	MXI1	chr5:27472141-27473942	Hela-S3	cervix:	n/a	n/a
23	MYC	chr5:27473174-27473236	Hela-S3	cervix:	n/a	n/a
24	RCOR1	chr5:27472053-27473819	Hela-S3	cervix:	n/a	n/a
25	RFX5	chr5:27472070-27474772	Hela-S3	cervix:	n/a	n/a
26	POLR2A	chr5:27473032-27473376	Hela-S3	cervix:	n/a	n/a
27	CHD2	chr5:27473143-27473297	HepG2	liver:	n/a	n/a
28	POLR2A	chr5:27472030-27473858	HepG2	liver:	n/a	n/a
29	POLR2A	chr5:27472998-27473374	GM12878	blood:	n/a	n/a
30	YY1	chr5:27472974-27473407	A549	lung:	n/a	chr5:27473203-27473215
31	MAX	chr5:27473055-27473334	H1-hESC	embryonic stem cell:	n/a	n/a
32	HEY1	chr5:27473041-27473295	HepG2	liver:	n/a	n/a
33	TBP	chr5:27472120-27473295	HepG2	liver:	n/a	n/a
34	POLR2A	chr5:27472083-27474198	Hela-S3	cervix:	n/a	n/a
35	GTF2F1	chr5:27472072-27474376	Hela-S3	cervix:	n/a	n/a
36	TBP	chr5:27473174-27473282	GM12878	blood:	n/a	n/a
37	POLR2A	chr5:27472092-27473400	H1-hESC	embryonic stem cell:	n/a	n/a
38	YY1	chr5:27473101-27473308	GM12891	blood:	n/a	chr5:27473203-27473215
39	MYC	chr5:27473187-27473296	K562	blood:	n/a	n/a
40	TBP	chr5:27472041-27473284	H1-hESC	embryonic stem cell:	n/a	n/a
41	BHLHE40	chr5:27473140-27473798	GM12878	blood:	n/a	n/a
42	POLR2A	chr5:27471861-27473974	H1-hESC	embryonic stem cell:	n/a	n/a
43	SIN3A	chr5:27472229-27473846	H1-hESC	embryonic stem cell:	n/a	n/a
44	MYC	chr5:27473046-27473876	K562	blood:	n/a	n/a
45	MAX	chr5:27472115-27474383	Hela-S3	cervix:	n/a	n/a
46	YY1	chr5:27473031-27473360	H1-hESC	embryonic stem cell:	n/a	chr5:27473203-27473215
47	POLR2A	chr5:27472107-27474257	Hela-S3	cervix:	n/a	n/a
48	MAX	chr5:27472926-27473963	A549	lung:	n/a	n/a
49	BHLHE40	chr5:27473085-27473935	K562	blood:	n/a	n/a
50	POLR2A	chr5:27473000-27473334	H1-hESC	embryonic stem cell:	n/a	n/a

No data

Variant related genes	Relation type
LINC01021	TF binding region

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10041105	0.93[EUR][1000 genomes]
rs10043278	0.92[EUR][1000 genomes]
rs10045438	0.92[EUR][1000 genomes]
rs10059093	0.91[EUR][1000 genomes]
rs10472571	0.92[EUR][1000 genomes]
rs10472572	0.92[EUR][1000 genomes]
rs10473841	0.93[EUR][1000 genomes]
rs10473842	0.92[EUR][1000 genomes]
rs10942252	0.94[EUR][1000 genomes]
rs10942259	0.84[EUR][1000 genomes]
rs11741407	0.84[EUR][1000 genomes]
rs11742648	0.94[EUR][1000 genomes]
rs11948589	0.84[EUR][1000 genomes]
rs11951177	0.92[EUR][1000 genomes]
rs12518672	0.86[EUR][1000 genomes]
rs12653531	0.92[EUR][1000 genomes]
rs12655436	0.93[EUR][1000 genomes]
rs12656885	0.86[EUR][1000 genomes]
rs12659482	0.90[EUR][1000 genomes]
rs12659906	0.84[EUR][1000 genomes]
rs13169053	0.80[EUR][1000 genomes]
rs2329584	0.92[EUR][1000 genomes]
rs2329622	0.85[EUR][1000 genomes]
rs2329626	0.84[EUR][1000 genomes]
rs35172002	0.94[EUR][1000 genomes]
rs56110024	0.84[EUR][1000 genomes]
rs62352269	0.84[EUR][1000 genomes]
rs6452387	0.86[EUR][1000 genomes]
rs6452390	0.84[EUR][1000 genomes]
rs6881731	0.84[EUR][1000 genomes]
rs6895283	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881286	chr5:27135351-27770554	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv880298	chr5:27193573-27659111	Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv880326	chr5:27193573-27743375	Transcr. at gene 5' and 3' Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv880623	chr5:27279981-27559659	Enhancers ZNF genes & repeats Strong transcription Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv881318	chr5:27323746-27559659	Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv881503	chr5:27344037-27510050	Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv881475	chr5:27376682-27510050	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv881003	chr5:27376682-27539490	Enhancers ZNF genes & repeats Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv880935	chr5:27376682-27559659	Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv880535	chr5:27376682-27706007	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
11	nsv881089	chr5:27387385-27478198	ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
12	nsv881139	chr5:27388559-27539490	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv880496	chr5:27388559-27559659	Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	nsv880940	chr5:27388559-27611431	Enhancers Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv880999	chr5:27388559-27770554	Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
16	nsv880926	chr5:27401935-27539490	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
17	nsv881221	chr5:27401935-27660532	Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
18	nsv881125	chr5:27406164-27622177	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
19	nsv880660	chr5:27418887-27510050	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	nsv880726	chr5:27424981-27539490	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv880474	chr5:27424981-27559659	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
22	nsv880869	chr5:27424981-27684515	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
23	nsv597681	chr5:27426728-27526060	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
24	nsv1030914	chr5:27458599-27502029	Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
25	nsv881364	chr5:27464184-27611431	Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:27471800-27474600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr5:27472000-27474800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:27472000-27474800	Active TSS	H1 Cell Line	embryonic stem cell
4	chr5:27472000-27475200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
5	chr5:27472200-27473400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr5:27472200-27474200	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr5:27472200-27474400	Active TSS	HUES48 Cell Line	embryonic stem cell
8	chr5:27472200-27474400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr5:27472200-27474400	Active TSS	K562	blood
10	chr5:27472200-27474600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:27472200-27474800	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr5:27472200-27475000	Active TSS	H9 Cell Line	embryonic stem cell
13	chr5:27472200-27475000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:27472200-27475200	Active TSS	A549	lung
15	chr5:27472200-27475400	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr5:27472200-27475400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr5:27472200-27475400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr5:27472400-27473400	Bivalent/Poised TSS	HepG2	liver
19	chr5:27472400-27473800	Active TSS	Osteobl	bone
20	chr5:27472400-27474000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr5:27472400-27474000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr5:27472400-27474400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr5:27472400-27474800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:27472400-27474800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr5:27472400-27475000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:27472400-27475000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:27472400-27475000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:27472400-27475000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:27472400-27475400	Active TSS	GM12878-XiMat	blood
30	chr5:27472600-27474400	Active TSS	Hela-S3	cervix
31	chr5:27472800-27474400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr5:27472800-27475000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:27473200-27473800	Active TSS	Liver	Liver
34	chr5:27473200-27474400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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