Variant report

Variant	rs7710717
Chromosome Location	chr5:43313942-43313943
allele	C/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	NFIC	chr5:43313690-43314087	HepG2	liver:	n/a	n/a
2	FOS	chr5:43313241-43314166	K562	blood:	n/a	chr5:43313584-43313593 chr5:43313642-43313651 chr5:43313341-43313352
3	MAX	chr5:43313409-43314268	A549	lung:	n/a	n/a
4	RFX5	chr5:43313126-43314121	Hela-S3	cervix:	n/a	chr5:43313984-43313993 chr5:43313800-43313815 chr5:43313979-43313995 chr5:43313982-43313996 chr5:43313627-43313641 chr5:43313980-43313994
5	POLR2A	chr5:43311701-43314619	GM12891	blood:	n/a	n/a
6	REST	chr5:43313138-43314123	HepG2	liver:	n/a	chr5:43313356-43313364
7	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
8	RUNX3	chr5:43312951-43314167	GM12878	blood:	n/a	n/a
9	SPI1	chr5:43313600-43313952	GM12878	blood:	n/a	n/a
10	POLR2A	chr5:43312347-43313959	K562	blood:	n/a	n/a
11	E2F6	chr5:43313359-43314019	H1-hESC	embryonic stem cell:	n/a	chr5:43313641-43313650 chr5:43313607-43313616 chr5:43313403-43313412
12	PBX3	chr5:43313623-43314006	GM12878	blood:	n/a	chr5:43313898-43313907
13	MYC	chr5:43312861-43314190	NB4	blood:	n/a	n/a
14	MAX	chr5:43313221-43314130	H1-hESC	embryonic stem cell:	n/a	n/a
15	USF2	chr5:43313663-43313979	Hela-S3	cervix:	n/a	n/a
16	RCOR1	chr5:43312792-43314015	GM12878	blood:	n/a	n/a
17	ELF1	chr5:43312974-43314056	GM12878	blood:	n/a	chr5:43313632-43313641 chr5:43313287-43313299
18	YY1	chr5:43313048-43313999	K562	blood:	n/a	chr5:43313635-43313649
19	POLR2A	chr5:43313815-43314146	SK-N-SH	brain:	n/a	n/a
20	MAFK	chr5:43313432-43314151	K562	blood:	n/a	n/a
21	ZNF384	chr5:43313350-43314020	K562	blood:	n/a	n/a
22	MAX	chr5:43313202-43314150	SK-N-SH	brain:	n/a	n/a
23	ELK1	chr5:43313432-43314085	K562	blood:	n/a	n/a
24	SIN3A	chr5:43312389-43314206	H1-hESC	embryonic stem cell:	n/a	chr5:43313637-43313646
25	ETS1	chr5:43313192-43313956	K562	blood:	n/a	chr5:43313403-43313414 chr5:43313759-43313766 chr5:43313758-43313772 chr5:43313759-43313770
26	MYBL2	chr5:43313122-43314372	HepG2	liver:	n/a	n/a
27	CREB1	chr5:43313422-43314069	ECC-1	luminal epithelium:	n/a	n/a
28	EP300	chr5:43313401-43314109	HepG2	liver:	n/a	n/a
29	TBP	chr5:43312927-43314065	K562	blood:	n/a	n/a
30	POLR2A	chr5:43313006-43314119	K562	blood:	n/a	n/a
31	CCNT2	chr5:43313173-43313960	K562	blood:	n/a	n/a
32	SIN3A	chr5:43312653-43314228	GM12878	blood:	n/a	chr5:43313637-43313646
33	CHD2	chr5:43312990-43314147	HepG2	liver:	n/a	n/a
34	ELF1	chr5:43312839-43314057	MCF-7	breast:	n/a	chr5:43313632-43313641 chr5:43313287-43313299
35	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
36	MYBL2	chr5:43312996-43314329	HepG2	liver:	n/a	n/a
37	TAF1	chr5:43312880-43314011	HepG2	liver:	n/a	n/a
38	REST	chr5:43313592-43314060	PFSK-1	brain:	n/a	n/a
39	EP300	chr5:43313210-43314196	GM12878	blood:	n/a	n/a
40	USF1	chr5:43313511-43313959	A549	lung:	n/a	chr5:43313634-43313650
41	TAF1	chr5:43312947-43314008	H1-neurons	neurons:	n/a	n/a
42	ZNF263	chr5:43312251-43314067	HEK293-T-REx	kidney:	n/a	chr5:43312540-43312561
43	BRCA1	chr5:43313634-43314122	H1-hESC	embryonic stem cell:	n/a	n/a
44	FOXM1	chr5:43313140-43314178	GM12878	blood:	n/a	n/a
45	SP1	chr5:43313191-43314133	GM12878	blood:	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
46	EP300	chr5:43313080-43314141	ECC-1	luminal epithelium:	n/a	n/a
47	BHLHE40	chr5:43312799-43314458	K562	blood:	n/a	chr5:43313634-43313650
48	POLR2A	chr5:43313045-43313973	MCF-7	breast:	n/a	n/a
49	MYC	chr5:43313240-43313943	HepG2	liver:	n/a	n/a
50	POLR2A	chr5:43313758-43314122	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:43120068..43123427-chr5:43312084..43315058,4	MCF-7	breast:
2	chr5:43313326..43314007-chr5:90676210..90676872,2	Hela-S3	cervix:
3	chr5:43311997..43315552-chr5:43481611..43486076,8	MCF-7	breast:
4	chr15:50646870..50647644-chr5:43312964..43313963,2	NB4	blood:
5	chr5:43230831..43233425-chr5:43313778..43315443,2	MCF-7	breast:
6	chr5:43119704..43122543-chr5:43311544..43313949,2	K562	blood:
7	chr5:43064535..43068771-chr5:43312463..43314872,5	MCF-7	breast:
8	chr5:43313320..43315914-chr5:43513861..43516716,3	MCF-7	breast:
9	chr5:43312211..43314783-chr5:43395042..43398709,5	MCF-7	breast:

Variant related genes	Relation type
HMGCS1	TF binding region
ENSG00000177738	Chromatin interaction
ENSG00000247763	Chromatin interaction
ENSG00000172244	Chromatin interaction
ENSG00000113369	Chromatin interaction
ENSG00000104064	Chromatin interaction
ENSG00000172262	Chromatin interaction
ENSG00000151881	Chromatin interaction
ENSG00000151882	Chromatin interaction
ENSG00000244879	Chromatin interaction
ENSG00000248240	Chromatin interaction
ENSG00000249492	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10037409	0.88[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10037706	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][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];0.83[YRI][hapmap];0.86[EUR][1000 genomes]
rs10052384	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10054415	1.00[CEU][hapmap];0.84[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];1.00[GIH][hapmap];1.00[MEX][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];0.84[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[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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	1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs6884349	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6887169	1.00[MEX][hapmap]
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[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][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]
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]
rs7729145	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];0.82[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs9292870	1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.88[YRI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9292872	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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];0.84[YRI][hapmap];0.86[EUR][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	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
4	esv1793502	chr5:43313178-43314216	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43310000-43314200	Active TSS	H1 Cell Line	embryonic stem cell
2	chr5:43310600-43314000	Active TSS	HSMMtube	muscle
3	chr5:43311000-43314000	Active TSS	Fetal Brain Male	brain
4	chr5:43311000-43314000	Active TSS	GM12878-XiMat	blood
5	chr5:43311400-43314200	Active TSS	NHLF	lung
6	chr5:43311800-43314200	Active TSS	Fetal Intestine Large	intestine
7	chr5:43312000-43314000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr5:43312000-43314000	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr5:43312000-43314000	Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr5:43312000-43314200	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr5:43312000-43314400	Active TSS	Fetal Muscle Trunk	muscle
12	chr5:43312200-43314000	Active TSS	Esophagus	oesophagus
13	chr5:43312200-43314200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr5:43312400-43314000	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr5:43312400-43314000	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr5:43312400-43314000	Active TSS	NHDF-Ad	bronchial
17	chr5:43312400-43314200	Active TSS	A549	lung
18	chr5:43312400-43314400	Active TSS	Ovary	ovary
19	chr5:43312600-43314000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:43312600-43314000	Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr5:43312600-43314000	Active TSS	HUES6 Cell Line	embryonic stem cell
22	chr5:43312600-43314000	Active TSS	iPS-20b Cell Line	embryonic stem cell
23	chr5:43312600-43314000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
24	chr5:43312600-43314000	Active TSS	Fetal Kidney	kidney
25	chr5:43312600-43314000	Active TSS	Left Ventricle	heart
26	chr5:43312600-43314000	Active TSS	Pancreas	Pancrea
27	chr5:43312600-43314000	Active TSS	HMEC	breast
28	chr5:43312600-43314000	Active TSS	HSMM	muscle
29	chr5:43312600-43314200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:43312600-43314200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:43312600-43314200	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr5:43312600-43314200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr5:43312600-43314200	Active TSS	Aorta	Aorta
34	chr5:43312600-43314200	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr5:43312600-43314200	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr5:43312600-43314400	Active TSS	Right Ventricle	heart
37	chr5:43312600-43314600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr5:43312800-43314000	Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr5:43312800-43314000	Active TSS	Primary T helper naive cells from peripheral blood	blood
40	chr5:43312800-43314000	Active TSS	Primary T killer naive cells fromperipheralblood	blood
41	chr5:43312800-43314000	Active TSS	Muscle Satellite Cultured Cells	--
42	chr5:43312800-43314000	Active TSS	Thymus	Thymus
43	chr5:43312800-43314000	Active TSS	HUVEC	blood vessel
44	chr5:43312800-43314000	Active TSS	Osteobl	bone
45	chr5:43312800-43314200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr5:43312800-43314200	Active TSS	Fetal Intestine Small	intestine
47	chr5:43312800-43314200	Active TSS	Placenta Amnion	Placenta Amnion
48	chr5:43312800-43314200	Active TSS	Psoas Muscle	Psoas
49	chr5:43312800-43314600	Active TSS	Brain Angular Gyrus	brain
50	chr5:43313000-43314000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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