Variant report

Variant	rs4713186
Chromosome Location	chr6:28909465-28909466
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	SP1	chr6:28908676-28909651	A549	lung:	n/a	n/a
2	MAFF	chr6:28908470-28909669	HepG2	liver:	n/a	n/a
3	TEAD4	chr6:28909184-28909709	A549	lung:	n/a	n/a
4	CEBPB	chr6:28908297-28909658	K562	blood:	n/a	n/a
5	SP1	chr6:28908625-28909634	A549	lung:	n/a	n/a
6	TEAD4	chr6:28908644-28909739	A549	lung:	n/a	n/a
7	E2F4	chr6:28909271-28909650	MCF10A-Er-Src	breast:	n/a	chr6:28909603-28909610
8	POLR3G	chr6:28908636-28909568	GM12878	blood:	n/a	n/a
9	IRF1	chr6:28908717-28909623	K562	blood:	n/a	chr6:28909310-28909324 chr6:28909305-28909318 chr6:28909291-28909303 chr6:28909305-28909318 chr6:28909307-28909321 chr6:28909305-28909318 chr6:28909307-28909317 chr6:28909313-28909327 chr6:28909311-28909324 chr6:28909303-28909317 chr6:28909313-28909323 chr6:28909309-28909323 chr6:28909313-28909324 chr6:28909304-28909318 chr6:28909305-28909318 chr6:28909307-28909328 chr6:28909311-28909324 chr6:28909305-28909325
10	FOXA1	chr6:28909148-28909627	HepG2	liver:	n/a	n/a
11	EP300	chr6:28908638-28909575	A549	lung:	n/a	chr6:28908717-28908726
12	MAX	chr6:28907738-28909821	HCT-116	colon:	n/a	n/a
13	NFIC	chr6:28908548-28909790	GM12878	blood:	n/a	n/a
14	UBTF	chr6:28908347-28909641	K562	blood:	n/a	n/a
15	IRF1	chr6:28908647-28909661	K562	blood:	n/a	chr6:28909310-28909324 chr6:28909305-28909318 chr6:28909291-28909303 chr6:28909305-28909318 chr6:28909307-28909321 chr6:28909305-28909318 chr6:28909307-28909317 chr6:28909313-28909327 chr6:28908715-28908735 chr6:28909311-28909324 chr6:28909303-28909317 chr6:28909313-28909323 chr6:28909309-28909323 chr6:28909313-28909324 chr6:28909304-28909318 chr6:28909305-28909318 chr6:28909307-28909328 chr6:28909311-28909324 chr6:28909305-28909325
16	ZNF143	chr6:28909327-28909536	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:28908626-28909536	Hela-S3	cervix:	n/a	n/a
18	CUX1	chr6:28908676-28909774	K562	blood:	n/a	n/a
19	POLR2A	chr6:28909184-28909577	PANC-1	pancreas:	n/a	n/a
20	USF1	chr6:28909256-28909579	A549	lung:	n/a	n/a
21	EP300	chr6:28908605-28909667	K562	blood:	n/a	chr6:28908717-28908726
22	MYC	chr6:28907422-28909659	K562	blood:	n/a	n/a
23	BCL11A	chr6:28909179-28909510	GM12878	blood:	n/a	chr6:28909307-28909316
24	BCLAF1	chr6:28908498-28909568	GM12878	blood:	n/a	chr6:28909307-28909316
25	JUND	chr6:28909294-28909465	HepG2	liver:	n/a	n/a
26	SMC3	chr6:28908656-28909565	Hela-S3	cervix:	n/a	n/a
27	MXI1	chr6:28908263-28909519	Hela-S3	cervix:	n/a	n/a
28	HNF4A	chr6:28909114-28909555	HepG2	liver:	n/a	n/a
29	ZNF384	chr6:28908559-28909722	K562	blood:	n/a	n/a
30	CEBPB	chr6:28909229-28909505	A549	lung:	n/a	n/a
31	TCF12	chr6:28907813-28909791	A549	lung:	n/a	n/a
32	MXI1	chr6:28908356-28909637	GM12878	blood:	n/a	n/a
33	CTCF	chr6:28908650-28909645	K562	blood:	n/a	chr6:28909477-28909486
34	STAT3	chr6:28908759-28909530	MCF10A-Er-Src	breast:	n/a	chr6:28909313-28909324
35	YY1	chr6:28909228-28909507	GM12892	blood:	n/a	chr6:28909459-28909471
36	BACH1	chr6:28908406-28909506	K562	blood:	n/a	chr6:28908660-28908674
37	CBX3	chr6:28908169-28909746	K562	blood:	n/a	n/a
38	MYC	chr6:28908395-28909652	NB4	blood:	n/a	n/a
39	FOSL2	chr6:28909155-28909623	HepG2	liver:	n/a	n/a
40	MBD4	chr6:28908525-28909681	HepG2	liver:	n/a	n/a
41	TEAD4	chr6:28907159-28910093	K562	blood:	n/a	n/a
42	EBF1	chr6:28908711-28909501	GM12878	blood:	n/a	n/a
43	EP300	chr6:28908555-28909559	GM12878	blood:	n/a	chr6:28908717-28908726
44	ATF2	chr6:28908503-28909638	GM12878	blood:	n/a	n/a
45	CEBPB	chr6:28908651-28909558	Hela-S3	cervix:	n/a	n/a
46	SIN3A	chr6:28907782-28910012	H1-hESC	embryonic stem cell:	n/a	n/a
47	TCF12	chr6:28909195-28909517	HepG2	liver:	n/a	n/a
48	GATA2	chr6:28908510-28909544	HUVEC	blood vessel:	n/a	n/a
49	BCLAF1	chr6:28908557-28909693	GM12878	blood:	n/a	chr6:28909307-28909316
50	YY1	chr6:28908992-28909526	GM12891	blood:	n/a	chr6:28909459-28909471

No.	Distal block	Cell Line	Cell type
1	chr6:28888957..28894217-chr6:28902105..28913114,27	MCF-7	breast:
2	chr6:28745229..28748097-chr6:28908724..28910861,2	K562	blood:
3	chr6:28859278..28869415-chr6:28906395..28912460,18	K562	blood:
4	chr6:28856688..28858917-chr6:28907185..28909608,2	K562	blood:
5	chr6:28908321..28911202-chr6:103515957..103517476,2	K562	blood:
6	chr6:28694415..28696951-chr6:28906885..28909854,2	K562	blood:
7	chr6:28806425..28808572-chr6:28907026..28910761,3	K562	blood:
8	chr6:28906972..28909678-chr6:28910352..28912254,2	MCF-7	breast:
9	chr6:28886838..28893375-chr6:28904762..28912890,19	K562	blood:
10	chr6:28907315..28909915-chr6:28920300..28923261,2	MCF-7	breast:
11	chr6:28907996..28910654-chr6:28948439..28951310,2	MCF-7	breast:
12	chr6:28907069..28909532-chr6:28910998..28913070,2	K562	blood:
13	chr6:28803772..28808857-chr6:28906937..28913057,11	K562	blood:
14	chr6:28844035..28846398-chr6:28907604..28909519,2	K562	blood:
15	chr6:28905933..28927444-chr6:28943937..28954526,53	K562	blood:
16	chr6:27775703..27777987-chr6:28908653..28911644,2	K562	blood:

Variant related genes	Relation type
C6orf100	TF binding region
ENSG00000225173	Chromatin interaction
ENSG00000224157	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000233366	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000263426	Chromatin interaction
ENSG00000227214	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1005123	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1237485	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1476016	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1543796	0.84[ASN][1000 genomes]
rs1794587	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs184093	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2013848	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2032500	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2071785	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2071790	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs209122	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs209126	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs209128	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs209129	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs209137	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs209138	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs209148	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs209149	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs209152	0.81[ASN][1000 genomes]
rs209153	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs209160	0.82[ASN][1000 genomes]
rs209161	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs209163	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs209164	0.81[ASN][1000 genomes]
rs2157312	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2157313	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2179648	0.83[ASN][1000 genomes]
rs2187807	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2187808	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2269555	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2394512	0.84[ASN][1000 genomes]
rs2765229	0.89[ASN][1000 genomes]
rs3129792	0.89[ASN][1000 genomes]
rs3129793	0.87[ASN][1000 genomes]
rs3130841	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3130842	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3130886	0.89[ASN][1000 genomes]
rs3130889	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3130897	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3131070	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3131074	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3131077	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3131100	0.81[ASN][1000 genomes]
rs3131102	0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3135303	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3135315	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3135321	0.89[ASN][1000 genomes]
rs3135322	0.89[ASN][1000 genomes]
rs3135323	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3135324	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3135326	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3135327	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3135328	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs381808	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs393431	0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs4427026	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4713187	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4713188	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713190	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4713192	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4947339	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6456876	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6456880	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6456883	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6456891	0.81[ASN][1000 genomes]
rs6901599	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6904975	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6906909	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6914955	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6916161	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6920392	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6927132	0.81[EUR][1000 genomes]
rs6931823	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs763009	0.93[ASN][1000 genomes]
rs7743189	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7755875	0.82[ASN][1000 genomes]
rs7761547	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7768299	0.84[ASN][1000 genomes]
rs9257401	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9257403	0.82[ASN][1000 genomes]
rs9257404	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9257405	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257408	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9257421	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9257447	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9257449	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9257455	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9257461	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9257464	0.81[EUR][1000 genomes]
rs9348816	0.84[ASN][1000 genomes]
rs9393939	0.84[ASN][1000 genomes]
rs9468467	0.86[ASN][1000 genomes]
rs9468472	0.81[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	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
3	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
4	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4713186	HIST1H2AE	cis	parietal	SCAN
rs4713186	ZNF323	cis	cerebellum	SCAN
rs4713186	ZKSCAN3	cis	cerebellum	SCAN
rs4713186	ZSCAN16	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28906600-28912600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr6:28907200-28910000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr6:28907200-28910000	Active TSS	K562	blood
4	chr6:28907400-28909600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr6:28907400-28909600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr6:28907400-28909800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:28907400-28909800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr6:28907400-28909800	Active TSS	GM12878-XiMat	blood
9	chr6:28907400-28909800	Active TSS	Hela-S3	cervix
10	chr6:28907400-28910000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr6:28907400-28910000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:28907400-28910000	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:28907400-28910000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr6:28907400-28910000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:28907400-28910200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr6:28907400-28910200	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr6:28907400-28910200	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr6:28907400-28910200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr6:28907400-28910200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr6:28907400-28910200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:28907400-28910200	Active TSS	Psoas Muscle	Psoas
22	chr6:28907400-28912400	Active TSS	H1 Cell Line	embryonic stem cell
23	chr6:28907400-28912400	Active TSS	H9 Cell Line	embryonic stem cell
24	chr6:28907400-28912400	Active TSS	iPS-18 Cell Line	embryonic stem cell
25	chr6:28907400-28912400	Active TSS	A549	lung
26	chr6:28907400-28912800	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr6:28907400-28913400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr6:28907600-28909800	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
29	chr6:28907600-28910000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
30	chr6:28907600-28910000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr6:28907600-28910200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:28907600-28910200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr6:28907600-28910200	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr6:28907600-28910200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
35	chr6:28907800-28909600	Active TSS	Aorta	Aorta
36	chr6:28907800-28909600	Active TSS	Brain Anterior Caudate	brain
37	chr6:28907800-28909600	Active TSS	Brain Cingulate Gyrus	brain
38	chr6:28907800-28909600	Active TSS	Brain Substantia Nigra	brain
39	chr6:28907800-28909600	Active TSS	Fetal Intestine Small	intestine
40	chr6:28907800-28909600	Active TSS	Fetal Lung	lung
41	chr6:28907800-28909600	Active TSS	NHLF	lung
42	chr6:28907800-28909600	Active TSS	Osteobl	bone
43	chr6:28907800-28909800	Active TSS	Brain Angular Gyrus	brain
44	chr6:28907800-28909800	Active TSS	Fetal Kidney	kidney
45	chr6:28907800-28909800	Active TSS	Right Atrium	heart
46	chr6:28907800-28909800	Active TSS	Right Ventricle	heart
47	chr6:28907800-28909800	Bivalent/Poised TSS	HepG2	liver
48	chr6:28907800-28910000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr6:28907800-28910000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:28907800-28910000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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