Variant report

Variant	rs7729145
Chromosome Location	chr5:43314232-43314233
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	MAX	chr5:43313409-43314268	A549	lung:	n/a	n/a
2	POLR2A	chr5:43311701-43314619	GM12891	blood:	n/a	n/a
3	RFX5	chr5:43313243-43314251	GM12878	blood:	n/a	chr5:43313984-43313993 chr5:43313800-43313815 chr5:43313979-43313995 chr5:43313982-43313996 chr5:43313627-43313641 chr5:43313980-43313994
4	MYBL2	chr5:43313122-43314372	HepG2	liver:	n/a	n/a
5	RFX5	chr5:43312424-43314698	SK-N-SH	brain:	n/a	chr5:43313984-43313993 chr5:43313800-43313815 chr5:43313979-43313995 chr5:43313982-43313996 chr5:43313627-43313641 chr5:43313980-43313994
6	MYBL2	chr5:43312996-43314329	HepG2	liver:	n/a	n/a
7	BHLHE40	chr5:43312799-43314458	K562	blood:	n/a	chr5:43313634-43313650
8	SREBP2	chr5:43313334-43314268	HepG2	liver:	n/a	n/a
9	NFYB	chr5:43313269-43314457	Hela-S3	cervix:	n/a	chr5:43313892-43313907 chr5:43313605-43313620 chr5:43313660-43313673 chr5:43313605-43313620
10	MXI1	chr5:43313440-43314293	K562	blood:	n/a	n/a
11	GATA3	chr5:43313153-43316032	A549	lung:	n/a	n/a
12	MAX	chr5:43312803-43315813	A549	lung:	n/a	n/a
13	CHD2	chr5:43312954-43314440	GM12878	blood:	n/a	n/a
14	SP1	chr5:43313045-43314248	HepG2	liver:	n/a	chr5:43313401-43313413 chr5:43313639-43313651 chr5:43313719-43313730 chr5:43313641-43313650 chr5:43313734-43313743 chr5:43313581-43313595 chr5:43313732-43313743 chr5:43313639-43313651 chr5:43313584-43313596
15	SP1	chr5:43313089-43315859	A549	lung:	n/a	chr5:43313401-43313413 chr5:43313639-43313651 chr5:43313719-43313730 chr5:43313641-43313650 chr5:43313734-43313743 chr5:43313581-43313595 chr5:43313732-43313743 chr5:43313639-43313651 chr5:43314998-43315008 chr5:43314275-43314288 chr5:43313584-43313596
16	NFYA	chr5:43313296-43314400	Hela-S3	cervix:	n/a	chr5:43313864-43313882 chr5:43313605-43313620 chr5:43313660-43313673 chr5:43313605-43313620
17	SP1	chr5:43312900-43314358	HCT-116	colon:	n/a	chr5:43313401-43313413 chr5:43313639-43313651 chr5:43313719-43313730 chr5:43313641-43313650 chr5:43313734-43313743 chr5:43313581-43313595 chr5:43313732-43313743 chr5:43313639-43313651 chr5:43314275-43314288 chr5:43313584-43313596
18	POLR2A	chr5:43312692-43314236	H1-neurons	neurons:	n/a	n/a
19	HEY1	chr5:43309230-43314247	HepG2	liver:	n/a	chr5:43313631-43313646 chr5:43313293-43313308 chr5:43313636-43313651
20	CBX3	chr5:43313148-43314468	K562	blood:	n/a	n/a
21	POLR2A	chr5:43312407-43314574	Raji	blood:	n/a	n/a
22	MAZ	chr5:43312484-43314464	IMR90	lung:	n/a	n/a
23	NFIC	chr5:43313496-43314291	HepG2	liver:	n/a	n/a
24	FOS	chr5:43313419-43314422	MCF10A-Er-Src	breast:	n/a	chr5:43313584-43313593 chr5:43313642-43313651
25	BHLHE40	chr5:43312830-43314310	GM12878	blood:	n/a	chr5:43313634-43313650
26	POLR2A	chr5:43313794-43314366	HepG2	liver:	n/a	n/a
27	RELA	chr5:43312469-43314357	GM18951	blood:	n/a	n/a
28	ATF2	chr5:43313146-43314252	GM12878	blood:	n/a	chr5:43313775-43313789
29	MXI1	chr5:43312825-43314456	HepG2	liver:	n/a	n/a
30	TBL1XR1	chr5:43313310-43314284	GM12878	blood:	n/a	n/a
31	FOSL2	chr5:43313366-43315985	A549	lung:	n/a	chr5:43313584-43313593 chr5:43314916-43314926 chr5:43313642-43313651 chr5:43314917-43314924 chr5:43314917-43314926
32	RELA	chr5:43312822-43314317	GM10847	blood:	n/a	n/a
33	MXI1	chr5:43312114-43314752	SK-N-SH	brain:	n/a	n/a
34	NFYA	chr5:43313311-43314520	K562	blood:	n/a	chr5:43313864-43313882 chr5:43313605-43313620 chr5:43313660-43313673 chr5:43313605-43313620
35	SIN3AK20	chr5:43312807-43314276	MCF-7	breast:	n/a	n/a
36	MTA3	chr5:43312708-43314632	GM12878	blood:	n/a	n/a
37	SREBP2	chr5:43312381-43314963	GM12878	blood:	n/a	n/a
38	E2F4	chr5:43313392-43314532	MCF10A-Er-Src	breast:	n/a	chr5:43313721-43313732 chr5:43314174-43314183 chr5:43314036-43314045 chr5:43313641-43313650 chr5:43313607-43313616 chr5:43313403-43313412
39	POLR2A	chr5:43309232-43314248	PBDE	blood:	n/a	n/a
40	FAM48A	chr5:43313644-43314323	GM12878	blood:	n/a	n/a
41	MAX	chr5:43313021-43314488	A549	lung:	n/a	n/a
42	CHD2	chr5:43313044-43314381	K562	blood:	n/a	n/a
43	NFYB	chr5:43312929-43314472	GM12878	blood:	n/a	chr5:43313892-43313907 chr5:43313605-43313620 chr5:43313660-43313673 chr5:43313605-43313620
44	PML	chr5:43313014-43314295	GM12878	blood:	n/a	n/a
45	RFX5	chr5:43313259-43314398	HepG2	liver:	n/a	chr5:43313984-43313993 chr5:43313800-43313815 chr5:43313979-43313995 chr5:43313982-43313996 chr5:43313627-43313641 chr5:43313980-43313994
46	TEAD4	chr5:43313031-43314422	K562	blood:	n/a	n/a
47	REST	chr5:43311938-43314784	H1-neurons	neurons:	n/a	chr5:43313356-43313364
48	SP1	chr5:43313147-43315875	A549	lung:	n/a	chr5:43313401-43313413 chr5:43313639-43313651 chr5:43313719-43313730 chr5:43313641-43313650 chr5:43313734-43313743 chr5:43313581-43313595 chr5:43313732-43313743 chr5:43313639-43313651 chr5:43314998-43315008 chr5:43314275-43314288 chr5:43313584-43313596
49	EP300	chr5:43313590-43315960	A549	lung:	n/a	chr5:43314917-43314926
50	NFIC	chr5:43314179-43314647	ECC-1	luminal epithelium:	n/a	chr5:43314408-43314425

No.	Distal block	Cell Line	Cell type
1	chr5:43120068..43123427-chr5:43312084..43315058,4	MCF-7	breast:
2	chr5:43311997..43315552-chr5:43481611..43486076,8	MCF-7	breast:
3	chr5:43230831..43233425-chr5:43313778..43315443,2	MCF-7	breast:
4	chr5:43064535..43068771-chr5:43312463..43314872,5	MCF-7	breast:
5	chr5:43313320..43315914-chr5:43513861..43516716,3	MCF-7	breast:
6	chr5:43312211..43314783-chr5:43395042..43398709,5	MCF-7	breast:

Variant related genes	Relation type
HMGCS1	TF binding region
ENSG00000248240	Chromatin interaction
ENSG00000249492	Chromatin interaction
ENSG00000172244	Chromatin interaction
ENSG00000151882	Chromatin interaction
ENSG00000177738	Chromatin interaction
ENSG00000151881	Chromatin interaction
ENSG00000247763	Chromatin interaction
ENSG00000172262	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10037409	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10037706	1.00[CEU][hapmap]
rs10038859	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10040897	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10043148	1.00[CEU][hapmap];0.84[YRI][hapmap];0.86[EUR][1000 genomes]
rs10052384	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10054415	1.00[CEU][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10056437	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10062031	0.86[EUR][1000 genomes]
rs10062121	0.86[EUR][1000 genomes]
rs10062598	1.00[CEU][hapmap];0.94[YRI][hapmap];0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10064967	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10067763	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10069507	1.00[CEU][hapmap]
rs10077324	1.00[EUR][1000 genomes]
rs10079530	1.00[EUR][1000 genomes]
rs10473306	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs10473308	1.00[CEU][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]
rs11955467	1.00[EUR][1000 genomes]
rs1478436	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16874093	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs16874094	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes]
rs28450849	0.86[EUR][1000 genomes]
rs28608156	0.91[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28688522	0.83[AFR][1000 genomes]
rs28856961	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs4326149	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs55645370	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60520238	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6865440	0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6884349	1.00[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6892413	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6893898	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6894240	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs6895237	1.00[CEU][hapmap];0.89[YRI][hapmap]
rs7356654	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73751075	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73751078	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73751082	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs73751083	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7710717	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7715267	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs7729140	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7733732	1.00[CEU][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292869	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9292870	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292872	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292875	1.00[CEU][hapmap];0.81[YRI][hapmap];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
2	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
3	nsv508352	chr5:43237830-43391062	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43312000-43314400	Active TSS	Fetal Muscle Trunk	muscle
2	chr5:43312400-43314400	Active TSS	Ovary	ovary
3	chr5:43312600-43314400	Active TSS	Right Ventricle	heart
4	chr5:43312600-43314600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:43312800-43314600	Active TSS	Brain Angular Gyrus	brain
6	chr5:43313000-43314400	Active TSS	Brain Substantia Nigra	brain
7	chr5:43313000-43314400	Active TSS	Colon Smooth Muscle	Colon
8	chr5:43313000-43314400	Active TSS	Duodenum Smooth Muscle	Duodenum
9	chr5:43313000-43314600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr5:43313600-43314400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
11	chr5:43313600-43314400	Active TSS	Right Atrium	heart
12	chr5:43313600-43314400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:43313800-43314400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr5:43313800-43314400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr5:43313800-43314400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
16	chr5:43313800-43314400	Flanking Active TSS	NHEK	skin
17	chr5:43313800-43314600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
18	chr5:43313800-43314600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr5:43313800-43314600	Flanking Active TSS	Dnd41	blood
20	chr5:43313800-43314600	Flanking Active TSS	K562	blood
21	chr5:43314000-43314400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr5:43314000-43314400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
23	chr5:43314000-43314400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
24	chr5:43314000-43314400	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr5:43314000-43314400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr5:43314000-43314400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
27	chr5:43314000-43314400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
28	chr5:43314000-43314400	Flanking Active TSS	Primary B cells from peripheral blood	blood
29	chr5:43314000-43314400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
30	chr5:43314000-43314400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
31	chr5:43314000-43314400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
32	chr5:43314000-43314400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr5:43314000-43314400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr5:43314000-43314400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr5:43314000-43314400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr5:43314000-43314400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
37	chr5:43314000-43314400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr5:43314000-43314400	Flanking Active TSS	Fetal Brain Male	brain
39	chr5:43314000-43314400	Flanking Active TSS	Fetal Kidney	kidney
40	chr5:43314000-43314400	Flanking Active TSS	Fetal Lung	lung
41	chr5:43314000-43314400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
42	chr5:43314000-43314400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr5:43314000-43314400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
44	chr5:43314000-43314400	Flanking Active TSS	Stomach Mucosa	stomach
45	chr5:43314000-43314400	Flanking Active TSS	HSMM	muscle
46	chr5:43314000-43314400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr5:43314000-43314400	Flanking Active TSS	NH-A	brain
48	chr5:43314000-43314400	Flanking Active TSS	NHDF-Ad	bronchial
49	chr5:43314000-43314600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr5:43314000-43314600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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