Variant report

Variant	rs1363513
Chromosome Location	chr5:179720380-179720381
allele	G/T
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	ESRRA	chr5:179720110-179721035	GM12878	blood:	n/a	chr5:179720583-179720595
2	MAZ	chr5:179717708-179721036	IMR90	lung:	n/a	chr5:179719295-179719302 chr5:179718302-179718312
3	SMC3	chr5:179720339-179720938	HepG2	liver:	n/a	chr5:179720683-179720697 chr5:179720683-179720690
4	CBX3	chr5:179720346-179720922	K562	blood:	n/a	n/a
5	MAX	chr5:179720341-179720878	NB4	blood:	n/a	n/a
6	EBF1	chr5:179720089-179720782	GM12878	blood:	n/a	chr5:179720193-179720206 chr5:179720193-179720204 chr5:179720195-179720204 chr5:179720195-179720205
7	CTCF	chr5:179720179-179721094	HCT-116	colon:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
8	CTCF	chr5:179720313-179720943	A549	lung:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
9	TCF12	chr5:179720319-179720829	A549	lung:	n/a	n/a
10	CTCF	chr5:179720353-179720827	LNCaP	prostate:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
11	MYC	chr5:179720309-179720878	MCF10A-Er-Src	breast:	n/a	n/a
12	BRCA1	chr5:179720366-179720851	HepG2	liver:	n/a	n/a
13	MYC	chr5:179720226-179720771	K562	blood:	n/a	n/a
14	NR2F2	chr5:179720239-179720886	K562	blood:	n/a	n/a
15	POLR2A	chr5:179720241-179720866	Hela-S3	cervix:	n/a	n/a
16	RAD21	chr5:179720306-179720985	A549	lung:	n/a	chr5:179720682-179720701 chr5:179720796-179720806
17	MAZ	chr5:179720151-179720864	K562	blood:	n/a	n/a
18	CTCF	chr5:179720117-179720833	HepG2	liver:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
19	RAD21	chr5:179720282-179720948	MCF-7	breast:	n/a	chr5:179720682-179720701 chr5:179720796-179720806
20	MAZ	chr5:179720249-179720879	GM12878	blood:	n/a	n/a
21	ZNF263	chr5:179720232-179720926	HEK293-T-REx	kidney:	n/a	chr5:179720634-179720655
22	CTCF	chr5:179720089-179720967	MCF-7	breast:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
23	E2F6	chr5:179720247-179721115	H1-hESC	embryonic stem cell:	n/a	n/a
24	CTCF	chr5:179720354-179720885	K562	blood:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
25	STAT3	chr5:179720346-179720805	GM12878	blood:	n/a	n/a
26	CEBPB	chr5:179719571-179720846	Hela-S3	cervix:	n/a	n/a
27	CTCF	chr5:179720154-179720943	GM12878	blood:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
28	POLR2A	chr5:179720365-179720779	Hela-S3	cervix:	n/a	n/a
29	EBF1	chr5:179720028-179720833	GM12878	blood:	n/a	chr5:179720193-179720206 chr5:179720193-179720204 chr5:179720195-179720204 chr5:179720195-179720205
30	BCLAF1	chr5:179720327-179720896	GM12878	blood:	n/a	n/a
31	RAD21	chr5:179720326-179720988	H1-hESC	embryonic stem cell:	n/a	chr5:179720682-179720701 chr5:179720796-179720806
32	CHD2	chr5:179720142-179720766	GM12878	blood:	n/a	chr5:179720169-179720179 chr5:179720164-179720174
33	RCOR1	chr5:179720244-179720835	K562	blood:	n/a	n/a
34	BRCA1	chr5:179720359-179720856	Hela-S3	cervix:	n/a	n/a
35	STAT3	chr5:179720333-179720542	MCF10A-Er-Src	breast:	n/a	n/a
36	MAX	chr5:179720103-179721008	A549	lung:	n/a	n/a
37	POLR2A	chr5:179720200-179720958	ECC-1	luminal epithelium:	n/a	n/a
38	CTCF	chr5:179720040-179721159	HCT-116	colon:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
39	CHD2	chr5:179720220-179720789	Hela-S3	cervix:	n/a	n/a
40	TCF12	chr5:179719977-179721065	A549	lung:	n/a	n/a
41	CTCF	chr5:179720363-179720902	IMR90	lung:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
42	YY1	chr5:179720295-179720886	H1-hESC	embryonic stem cell:	n/a	n/a
43	RCOR1	chr5:179720375-179720900	K562	blood:	n/a	n/a
44	MXI1	chr5:179720316-179720818	Hela-S3	cervix:	n/a	n/a
45	MYC	chr5:179720354-179720836	MCF10A-Er-Src	breast:	n/a	n/a
46	CTCF	chr5:179720085-179721305	SK-N-SH	brain:	n/a	chr5:179720684-179720693 chr5:179720681-179720699 chr5:179720683-179720704 chr5:179720682-179720698
47	POLR2A	chr5:179720010-179721145	SK-N-MC	brain:	n/a	n/a
48	ELF1	chr5:179720042-179720778	GM12878	blood:	n/a	n/a
49	JUN	chr5:179720038-179720984	K562	blood:	n/a	chr5:179720162-179720171
50	RCOR1	chr5:179720261-179720844	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:179718755..179721306-chr5:179919977..179922949,4	MCF-7	breast:
2	chr5:179628129..179628639-chr5:179720355..179721073,2	MCF-7	breast:
3	chr5:179683447..179685223-chr5:179718038..179720496,2	MCF-7	breast:
4	chr5:179720287..179721046-chr5:179740621..179741577,2	MCF-7	breast:
5	chr5:179720249..179721437-chr5:179755481..179756336,5	K562	blood:
6	chr5:179718262..179720717-chr5:180237170..180239607,2	MCF-7	breast:
7	chr5:179720259..179720769-chrX:4912894..4913414,2	MCF-7	breast:
8	chr5:179720303..179721088-chr5:179756913..179757480,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CNOT6-4	chr5:179720245-179720418	XLOC_004678
2	lnc-CNOT6-4	chr5:179719184-179722539	NONHSAT105673

Variant related genes	Relation type
MAPK9	TF binding region
ENSG00000113300	Chromatin interaction
ENSG00000131446	Chromatin interaction
ENSG00000253908	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12653720	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12654184	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12659522	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35013759	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3749795	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3749796	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription 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 miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
3	esv2758032	chr5:179534477-179729944	Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	esv2759398	chr5:179534477-179729944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1023914	chr5:179649883-180040672	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
6	nsv537983	chr5:179649883-180040672	Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
7	nsv1030697	chr5:179710469-180686563	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	184 gene(s)	inside rSNPs	diseases
8	nsv883290	chr5:179712060-179818868	Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	esv3398259	chr5:179717146-179721444	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv830563	chr5:179717693-179898609	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	nsv10787	chr5:179717724-179732388	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
12	esv3437532	chr5:179717871-179720719	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 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	chr5:179717600-179720600	Active TSS	Aorta	Aorta
2	chr5:179717800-179720400	Active TSS	H9 Cell Line	embryonic stem cell
3	chr5:179717800-179720400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr5:179717800-179720600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:179717800-179720600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr5:179717800-179720600	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr5:179718000-179720400	Active TSS	iPS-15b Cell Line	embryonic stem cell
8	chr5:179718000-179720600	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr5:179718200-179720400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr5:179718200-179720400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr5:179718200-179720600	Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr5:179718200-179720600	Active TSS	HSMM	muscle
13	chr5:179718200-179720800	Active TSS	Rectal Smooth Muscle	rectum
14	chr5:179718200-179721000	Active TSS	Fetal Kidney	kidney
15	chr5:179719200-179720400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
16	chr5:179719200-179720600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr5:179719600-179720400	Flanking Active TSS	Primary B cells from peripheral blood	blood
18	chr5:179719600-179720400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr5:179719600-179720600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
20	chr5:179719600-179720600	Flanking Active TSS	Primary T cells fromperipheralblood	blood
21	chr5:179719600-179720600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
22	chr5:179719600-179720600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr5:179719600-179720600	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr5:179719600-179720600	Flanking Active TSS	Fetal Muscle Leg	muscle
25	chr5:179719600-179720800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr5:179719600-179720800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:179719800-179720400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
28	chr5:179719800-179720400	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr5:179719800-179720600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr5:179719800-179720800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr5:179719800-179720800	Flanking Active TSS	Dnd41	blood
32	chr5:179720000-179720400	Flanking Active TSS	Brain Germinal Matrix	brain
33	chr5:179720000-179720400	Flanking Active TSS	Placenta	Placenta
34	chr5:179720000-179720400	Flanking Active TSS	Fetal Thymus	thymus
35	chr5:179720000-179720600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr5:179720000-179720600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr5:179720000-179720600	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr5:179720000-179720600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
39	chr5:179720000-179720600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
40	chr5:179720000-179720600	Flanking Active TSS	Liver	Liver
41	chr5:179720000-179720600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
42	chr5:179720000-179720600	Enhancers	Lung	lung
43	chr5:179720000-179720600	Enhancers	Psoas Muscle	Psoas
44	chr5:179720000-179720600	Enhancers	Right Ventricle	heart
45	chr5:179720000-179720600	Flanking Active TSS	Osteobl	bone
46	chr5:179720000-179720800	Enhancers	Placenta Amnion	Placenta Amnion
47	chr5:179720000-179720800	Genic enhancers	Right Atrium	heart
48	chr5:179720000-179721000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr5:179720000-179721000	Enhancers	Fetal Muscle Trunk	muscle
50	chr5:179720000-179721000	Enhancers	Small Intestine	intestine

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