Variant report

Variant	rs39794
Chromosome Location	chr5:40834433-40834434
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:168)
CpG islands
(count:0)
Chromatin interactive
region (count:20)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:168 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:40833886-40836321	GM12891	blood:	n/a	n/a
2	POLR2A	chr5:40824786-40836349	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr5:40833397-40836297	GM15510	blood:	n/a	n/a
4	MAZ	chr5:40834190-40836857	K562	blood:	n/a	n/a
5	POLR2A	chr5:40833540-40836475	HL-60	blood:	n/a	n/a
6	GTF2F1	chr5:40834330-40836510	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr5:40830800-40836632	NB4	blood:	n/a	n/a
8	MYC	chr5:40833754-40836963	K562	blood:	n/a	n/a
9	POLR2A	chr5:40832709-40836399	GM18951	blood:	n/a	n/a
10	CHD2	chr5:40834004-40836006	K562	blood:	n/a	n/a
11	POLR2A	chr5:40833813-40836384	H1-hESC	embryonic stem cell:	n/a	n/a
12	SIX5	chr5:40834050-40834830	H1-hESC	embryonic stem cell:	n/a	n/a
13	POLR2A	chr5:40824383-40836719	K562	blood:	n/a	n/a
14	POLR2A	chr5:40832572-40835811	U87	brain:	n/a	n/a
15	ELK1	chr5:40834311-40834563	GM12878	blood:	n/a	n/a
16	BCLAF1	chr5:40834289-40835944	GM12878	blood:	n/a	chr5:40835371-40835380 chr5:40835329-40835338
17	POLR2A	chr5:40823520-40836317	SK-N-MC	brain:	n/a	n/a
18	IRF1	chr5:40833040-40835975	K562	blood:	n/a	chr5:40835569-40835581 chr5:40834809-40834822 chr5:40835564-40835581 chr5:40835569-40835580 chr5:40834809-40834823 chr5:40835569-40835581
19	POLR2A	chr5:40829918-40836581	Hela-S3	cervix:	n/a	n/a
20	SP1	chr5:40834068-40834930	H1-hESC	embryonic stem cell:	n/a	n/a
21	MXI1	chr5:40834033-40835793	GM12878	blood:	n/a	n/a
22	POLR2A	chr5:40833859-40835989	GM12891	blood:	n/a	n/a
23	POLR2A	chr5:40833129-40836609	GM12878	blood:	n/a	n/a
24	POLR2A	chr5:40833996-40836057	H1-hESC	embryonic stem cell:	n/a	n/a
25	PML	chr5:40833820-40836144	K562	blood:	n/a	chr5:40835321-40835329
26	WRNIP1	chr5:40833235-40836410	GM12878	blood:	n/a	n/a
27	POLR2A	chr5:40834076-40834500	HepG2	liver:	n/a	n/a
28	GATA3	chr5:40834103-40834861	T-47D	breast:	n/a	n/a
29	POLR2A	chr5:40833681-40836203	HUVEC	blood vessel:	n/a	n/a
30	IRF1	chr5:40834129-40836010	K562	blood:	n/a	chr5:40835569-40835581 chr5:40834809-40834822 chr5:40835564-40835581 chr5:40835569-40835580 chr5:40834809-40834823 chr5:40835569-40835581
31	POLR2A	chr5:40832988-40835995	GM12892	blood:	n/a	n/a
32	POLR2A	chr5:40833376-40836533	Hela-S3	cervix:	n/a	n/a
33	TBP	chr5:40834228-40836790	Hela-S3	cervix:	n/a	n/a
34	MTA3	chr5:40834238-40835893	GM12878	blood:	n/a	n/a
35	POLR2A	chr5:40834192-40835809	ECC-1	luminal epithelium:	n/a	n/a
36	USF2	chr5:40833426-40836685	Hela-S3	cervix:	n/a	n/a
37	POLR2A	chr5:40832742-40836593	PANC-1	pancreas:	n/a	n/a
38	GABPA	chr5:40834089-40836341	A549	lung:	n/a	n/a
39	POLR2A	chr5:40826353-40836595	GM12878	blood:	n/a	n/a
40	POLR2A	chr5:40825968-40836481	GM12878	blood:	n/a	n/a
41	POLR2A	chr5:40833851-40835849	HCT-116	colon:	n/a	n/a
42	HEY1	chr5:40834177-40834730	HepG2	liver:	n/a	n/a
43	SMARCB1	chr5:40833425-40836418	Hela-S3	cervix:	n/a	n/a
44	TBP	chr5:40834272-40835972	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr5:40824347-40836356	U87	brain:	n/a	n/a
46	MTA3	chr5:40834102-40836016	GM12878	blood:	n/a	n/a
47	RELA	chr5:40834089-40836053	GM18505	blood:	n/a	n/a
48	POLR2A	chr5:40833106-40836648	K562	blood:	n/a	n/a
49	POLR2A	chr5:40833006-40836182	MCF-7	breast:	n/a	n/a
50	EP300	chr5:40833659-40836504	K562	blood:	n/a	n/a

No data

(count:20 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:40753631..40759305-chr5:40833742..40838306,12	K562	blood:
2	chr17:8198296..8199051-chr5:40833703..40834545,2	Hela-S3	cervix:
3	chr1:149900207..149902355-chr5:40832606..40834765,2	MCF-7	breast:
4	chr5:40762484..40765387-chr5:40833487..40838148,4	K562	blood:
5	chr5:40834401..40835296-chr5:43483773..43484582,2	Hela-S3	cervix:
6	chr5:40753823..40758906-chr5:40833676..40836936,8	MCF-7	breast:
7	chr5:40795843..40803356-chr5:40833207..40837160,32	MCF-7	breast:
8	chr18:9474867..9475442-chr5:40834265..40834948,2	Hela-S3	cervix:
9	chr5:40833991..40836420-chr5:41902681..41904929,3	K562	blood:
10	chr5:40833974..40834885-chr6:31508984..31509608,2	Hela-S3	cervix:
11	chr5:40752902..40758869-chr5:40832024..40838409,16	K562	blood:
12	chr5:40789707..40791650-chr5:40833757..40835320,2	K562	blood:
13	chr5:40760388..40764938-chr5:40832988..40836769,5	MCF-7	breast:
14	chr1:149858456..149859986-chr5:40833944..40836674,2	MCF-7	breast:
15	chr5:40796430..40799942-chr5:40831748..40836996,14	MCF-7	breast:
16	chr12:48448475..48449474-chr5:40834158..40834864,2	Hela-S3	cervix:
17	chr5:40790254..40794130-chr5:40832238..40836861,6	MCF-7	breast:
18	chr14:53257908..53258576-chr5:40834406..40835365,2	Hela-S3	cervix:
19	chr11:63580858..63581436-chr5:40834265..40835260,2	Hela-S3	cervix:
20	chr5:40752681..40758776-chr5:40831589..40836413,12	MCF-7	breast:

No data

Variant related genes	Relation type
RPL37	TF binding region
SNORD72	TF binding region
ENSG00000125434	Chromatin interaction
ENSG00000113638	Chromatin interaction
ENSG00000143368	Chromatin interaction
ENSG00000205765	Chromatin interaction
ENSG00000100522	Chromatin interaction
ENSG00000184260	Chromatin interaction
ENSG00000184270	Chromatin interaction
ENSG00000178096	Chromatin interaction
ENSG00000198563	Chromatin interaction
ENSG00000168005	Chromatin interaction
ENSG00000132356	Chromatin interaction
ENSG00000151881	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000212567	Chromatin interaction
ENSG00000240399	Chromatin interaction
ENSG00000017797	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10064232	0.88[ASN][1000 genomes]
rs1070445	0.94[ASN][1000 genomes]
rs1097592	0.94[ASN][1000 genomes]
rs1097604	0.94[ASN][1000 genomes]
rs1530811	0.88[ASN][1000 genomes]
rs154272	0.88[ASN][1000 genomes]
rs154273	1.00[ASN][1000 genomes]
rs154274	0.94[ASN][1000 genomes]
rs1631661	1.00[ASN][1000 genomes]
rs1645509	0.88[ASN][1000 genomes]
rs166282	0.88[ASN][1000 genomes]
rs1697929	0.94[ASN][1000 genomes]
rs1697937	0.94[ASN][1000 genomes]
rs173619	0.88[ASN][1000 genomes]
rs181819	0.82[ASN][1000 genomes]
rs181820	0.88[ASN][1000 genomes]
rs181821	0.88[ASN][1000 genomes]
rs1833892	0.88[ASN][1000 genomes]
rs184436	0.94[ASN][1000 genomes]
rs187274	0.88[ASN][1000 genomes]
rs192962	0.94[ASN][1000 genomes]
rs2262009	0.94[ASN][1000 genomes]
rs249408	0.81[ASN][1000 genomes]
rs249409	0.81[ASN][1000 genomes]
rs249411	0.81[ASN][1000 genomes]
rs249412	0.81[ASN][1000 genomes]
rs249439	0.88[ASN][1000 genomes]
rs249443	1.00[ASN][1000 genomes]
rs249444	1.00[ASN][1000 genomes]
rs29762	1.00[ASN][1000 genomes]
rs29763	1.00[ASN][1000 genomes]
rs29764	1.00[ASN][1000 genomes]
rs323554	0.88[ASN][1000 genomes]
rs323556	0.94[ASN][1000 genomes]
rs323560	0.94[ASN][1000 genomes]
rs323562	0.94[ASN][1000 genomes]
rs34236150	0.88[ASN][1000 genomes]
rs370346	0.88[ASN][1000 genomes]
rs396412	0.88[ASN][1000 genomes]
rs408238	0.88[ASN][1000 genomes]
rs4129381	0.81[ASN][1000 genomes]
rs418494	0.94[ASN][1000 genomes]
rs424787	0.88[ASN][1000 genomes]
rs42515	1.00[ASN][1000 genomes]
rs433730	0.94[ASN][1000 genomes]
rs438604	0.88[ASN][1000 genomes]
rs441016	0.88[ASN][1000 genomes]
rs442869	0.88[ASN][1000 genomes]
rs445367	0.88[ASN][1000 genomes]
rs455374	0.88[ASN][1000 genomes]
rs457111	0.88[ASN][1000 genomes]
rs458884	0.88[ASN][1000 genomes]
rs459491	0.88[ASN][1000 genomes]
rs459794	0.88[ASN][1000 genomes]
rs460752	0.88[ASN][1000 genomes]
rs463040	0.88[ASN][1000 genomes]
rs463675	0.88[ASN][1000 genomes]
rs463905	0.88[ASN][1000 genomes]
rs464045	0.88[ASN][1000 genomes]
rs464191	0.88[ASN][1000 genomes]
rs465467	0.88[ASN][1000 genomes]
rs466960	1.00[ASN][1000 genomes]
rs467438	0.88[ASN][1000 genomes]
rs694217	0.88[ASN][1000 genomes]
rs7717507	0.88[ASN][1000 genomes]
rs837119	0.81[ASN][1000 genomes]
rs837378	0.94[ASN][1000 genomes]
rs837381	0.94[ASN][1000 genomes]
rs837382	0.94[ASN][1000 genomes]
rs837384	0.94[ASN][1000 genomes]
rs837385	0.94[ASN][1000 genomes]
rs837389	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases
2	nsv597877	chr5:40796746-40848803	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	158 gene(s)	inside rSNPs	diseases
3	nsv518711	chr5:40827307-40835627	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	137 gene(s)	inside rSNPs	diseases
4	nsv968907	chr5:40832497-40834810	Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40830200-40834800	Transcr. at gene 5' and 3'	Hela-S3	cervix
2	chr5:40831400-40834600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr5:40831400-40835000	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:40831600-40835000	Transcr. at gene 5' and 3'	K562	blood
5	chr5:40831800-40834800	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
6	chr5:40831800-40835000	Transcr. at gene 5' and 3'	A549	lung
7	chr5:40831800-40835200	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
8	chr5:40832000-40835000	Transcr. at gene 5' and 3'	iPS-15b Cell Line	embryonic stem cell
9	chr5:40832000-40835200	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
10	chr5:40832200-40834600	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr5:40832200-40834600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr5:40832200-40834600	Transcr. at gene 5' and 3'	HUVEC	blood vessel
13	chr5:40832200-40834600	Transcr. at gene 5' and 3'	NH-A	brain
14	chr5:40832200-40835000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
15	chr5:40832200-40835000	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
16	chr5:40832400-40834800	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
17	chr5:40832600-40834600	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
18	chr5:40832600-40834600	Transcr. at gene 5' and 3'	HMEC	breast
19	chr5:40832600-40834800	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
20	chr5:40832600-40834800	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
21	chr5:40832600-40834800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr5:40832600-40835200	Transcr. at gene 5' and 3'	Muscle Satellite Cultured Cells	--
23	chr5:40832800-40834600	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:40832800-40834600	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr5:40832800-40834800	Transcr. at gene 5' and 3'	Osteobl	bone
26	chr5:40832800-40835000	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr5:40832800-40835000	Transcr. at gene 5' and 3'	NHLF	lung
28	chr5:40833000-40835000	Transcr. at gene 5' and 3'	NHEK	skin
29	chr5:40833200-40834600	Transcr. at gene 5' and 3'	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr5:40833200-40834600	Transcr. at gene 5' and 3'	ES-UCSF4 Cell Line	embryonic stem cell
31	chr5:40833200-40834600	Transcr. at gene 5' and 3'	Primary T killer memory cells from peripheral blood	blood
32	chr5:40833200-40834800	Transcr. at gene 5' and 3'	H9 Cell Line	embryonic stem cell
33	chr5:40833200-40834800	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:40833200-40834800	Transcr. at gene 5' and 3'	Fetal Thymus	thymus
35	chr5:40833200-40834800	Transcr. at gene 5' and 3'	HSMM	muscle
36	chr5:40833200-40835000	Transcr. at gene 5' and 3'	Dnd41	blood
37	chr5:40833200-40835200	Transcr. at gene 5' and 3'	H1 Cell Line	embryonic stem cell
38	chr5:40833200-40835200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
39	chr5:40833200-40835400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
40	chr5:40833200-40836400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr5:40833400-40834600	Transcr. at gene 5' and 3'	Fetal Stomach	stomach
42	chr5:40833400-40834800	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr5:40833400-40836000	Active TSS	Right Ventricle	heart
44	chr5:40833400-40836200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr5:40833600-40834600	Transcr. at gene 5' and 3'	Adipose Nuclei	Adipose
46	chr5:40833600-40834800	Transcr. at gene 5' and 3'	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr5:40833600-40836000	Flanking Active TSS	Primary hematopoietic stem cells	blood
48	chr5:40833600-40836200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr5:40833600-40836600	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr5:40833800-40834600	Transcr. at gene 5' and 3'	Fetal Lung	lung

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