Variant report

Variant	rs3756996
Chromosome Location	chr6:127664258-127664259
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:378)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:378 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:127663973-127665467	GM12892	blood:	n/a	n/a
2	ELF1	chr6:127664052-127665042	SK-N-SH	brain:	n/a	chr6:127664696-127664707
3	PML	chr6:127664095-127665097	K562	blood:	n/a	n/a
4	REST	chr6:127664004-127665037	HL-60	blood:	n/a	chr6:127664482-127664502 chr6:127664482-127664502
5	SIN3AK20	chr6:127664015-127665066	HCT-116	colon:	n/a	n/a
6	MTA3	chr6:127663895-127665460	GM12878	blood:	n/a	n/a
7	POLR2A	chr6:127664179-127664846	A549	lung:	n/a	n/a
8	POLR2A	chr6:127664057-127665039	HUVEC	blood vessel:	n/a	n/a
9	MXI1	chr6:127662422-127665983	IMR90	lung:	n/a	n/a
10	PAX5	chr6:127664205-127664793	GM12878	blood:	n/a	n/a
11	BHLHE40	chr6:127663705-127665355	HepG2	liver:	n/a	n/a
12	E2F6	chr6:127663941-127665024	H1-hESC	embryonic stem cell:	n/a	chr6:127664554-127664563
13	GATA3	chr6:127664174-127664984	A549	lung:	n/a	chr6:127664646-127664656
14	YY1	chr6:127664102-127664871	GM12891	blood:	n/a	n/a
15	CREB1	chr6:127663404-127665009	HepG2	liver:	n/a	n/a
16	TCF12	chr6:127664199-127664609	GM12878	blood:	n/a	n/a
17	POLR2A	chr6:127663681-127665874	K562	blood:	n/a	n/a
18	POLR2A	chr6:127662633-127665925	HepG2	liver:	n/a	n/a
19	ATF2	chr6:127664002-127665056	GM12878	blood:	n/a	n/a
20	TBP	chr6:127663633-127665883	K562	blood:	n/a	n/a
21	POLR2A	chr6:127664163-127664989	MCF-7	breast:	n/a	n/a
22	HEY1	chr6:127664151-127664982	K562	blood:	n/a	n/a
23	TBP	chr6:127664211-127665400	H1-hESC	embryonic stem cell:	n/a	n/a
24	HCFC1	chr6:127664028-127665782	K562	blood:	n/a	n/a
25	POLR2A	chr6:127664158-127664905	MCF-7	breast:	n/a	n/a
26	CTCF	chr6:127664238-127664329	MCF-7	breast:	n/a	n/a
27	KAP1	chr6:127663950-127665656	U2OS	brain:	n/a	n/a
28	TCF7L2	chr6:127664196-127664743	MCF-7	breast:	n/a	n/a
29	MYBL2	chr6:127663618-127665770	HepG2	liver:	n/a	n/a
30	BHLHE40	chr6:127664167-127665421	GM12878	blood:	n/a	n/a
31	BACH1	chr6:127664178-127664955	H1-hESC	embryonic stem cell:	n/a	n/a
32	E2F4	chr6:127664064-127664911	MCF10A-Er-Src	breast:	n/a	chr6:127664554-127664563
33	POLR2A	chr6:127664152-127665412	SK-N-MC	brain:	n/a	n/a
34	TAF1	chr6:127664123-127665026	K562	blood:	n/a	n/a
35	MAX	chr6:127664046-127664863	K562	blood:	n/a	n/a
36	POLR2A	chr6:127662974-127665790	GM19099	blood:	n/a	n/a
37	POLR2A	chr6:127663695-127665466	GM18951	blood:	n/a	n/a
38	FOXM1	chr6:127664056-127665058	GM12878	blood:	n/a	n/a
39	MAX	chr6:127664002-127665071	ECC-1	luminal epithelium:	n/a	n/a
40	TAF1	chr6:127664132-127664841	HepG2	liver:	n/a	n/a
41	CTCF	chr6:127664245-127664396	MCF-7	breast:	n/a	n/a
42	ARID3A	chr6:127663395-127665038	HepG2	liver:	n/a	n/a
43	POLR2A	chr6:127664112-127664987	K562	blood:	n/a	n/a
44	MAX	chr6:127663613-127665022	K562	blood:	n/a	n/a
45	POLR2A	chr6:127662989-127665867	K562	blood:	n/a	n/a
46	CTCF	chr6:127664180-127664330	NHLF	lung:	n/a	n/a
47	MYC	chr6:127663841-127665216	K562	blood:	n/a	n/a
48	ZBTB33	chr6:127663973-127664323	HepG2	liver:	n/a	n/a
49	PML	chr6:127664122-127664990	GM12878	blood:	n/a	n/a
50	POLR2A	chr6:127664210-127664912	SK-N-SH	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:103577308..103578043-chr6:127664124..127665002,2	Hela-S3	cervix:
2	chr6:127638086..127642248-chr6:127662682..127665372,3	K562	blood:
3	chr6:127586572..127589762-chr6:127662304..127666058,6	K562	blood:
4	chr6:127663267..127665190-chr6:127682385..127684934,2	MCF-7	breast:
5	chr6:127638086..127640827-chr6:127662682..127665250,2	K562	blood:
6	chr6:127586417..127590637-chr6:127662350..127666578,4	K562	blood:
7	chr6:127647745..127649356-chr6:127662389..127665188,2	K562	blood:

No data

Variant related genes	Relation type
ECHDC1	TF binding region
ENSG00000198408	Chromatin interaction
ENSG00000251768	Chromatin interaction
ENSG00000118518	Chromatin interaction
ENSG00000220744	Chromatin interaction
ENSG00000093144	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1073931	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1073932	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10872312	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13218061	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1543432	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1964130	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2038378	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2057223	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2144742	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2144743	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2180341	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2281491	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2326567	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2875972	0.82[AMR][1000 genomes]
rs3798850	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3798852	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3798857	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4280986	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4448121	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4472373	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4486042	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4895821	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4895822	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4895823	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4897207	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569477	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569478	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569479	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569480	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569482	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6569483	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6569486	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67371475	0.82[EUR][1000 genomes]
rs6900074	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6903878	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6904520	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6904630	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6906717	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6910763	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6913424	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6916990	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6930849	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6937287	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7449576	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7745944	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7751865	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7752238	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7753913	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7756336	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7756880	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7756884	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7760748	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7766942	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7771923	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7773484	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7774468	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7775493	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7776136	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs877661	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs910720	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9285459	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9285460	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9321073	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9321074	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9321076	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9321079	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9375499	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9375501	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9375503	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9385419	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9388553	0.80[EUR][1000 genomes]
rs9388555	0.80[EUR][1000 genomes]
rs9388561	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9388568	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9388571	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9398836	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9398837	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9398838	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9398839	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9398840	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9398841	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9398842	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9401950	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9401951	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9401952	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9401953	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv604641	chr6:127657099-127719062	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3756996	ECHDC1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:127661600-127666000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:127662000-127665600	Active TSS	Right Atrium	heart
3	chr6:127662600-127664600	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr6:127662600-127665800	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr6:127662800-127665600	Active TSS	H9 Cell Line	embryonic stem cell
6	chr6:127662800-127665600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:127662800-127665600	Active TSS	Lung	lung
8	chr6:127662800-127665800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:127662800-127665800	Active TSS	Aorta	Aorta
10	chr6:127662800-127665800	Active TSS	Ovary	ovary
11	chr6:127663000-127665600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr6:127663200-127665400	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:127663200-127665600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr6:127663200-127665600	Active TSS	Fetal Muscle Trunk	muscle
15	chr6:127663200-127665600	Active TSS	GM12878-XiMat	blood
16	chr6:127663200-127665600	Active TSS	HSMMtube	muscle
17	chr6:127663200-127665800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr6:127663200-127666000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:127663400-127665400	Active TSS	Fetal Heart	heart
20	chr6:127663400-127665600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:127663400-127665600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr6:127663400-127665600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:127663400-127665600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr6:127663400-127665600	Active TSS	Left Ventricle	heart
25	chr6:127663400-127665600	Active TSS	Pancreas	Pancrea
26	chr6:127663400-127665600	Active TSS	HSMM	muscle
27	chr6:127663400-127665600	Active TSS	NHDF-Ad	bronchial
28	chr6:127663400-127665800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr6:127663400-127665800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr6:127663400-127665800	Active TSS	Colonic Mucosa	Colon
31	chr6:127663400-127665800	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr6:127663400-127665800	Active TSS	Right Ventricle	heart
33	chr6:127663400-127666000	Active TSS	H1 Cell Line	embryonic stem cell
34	chr6:127663400-127666000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:127663400-127666000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr6:127663600-127665400	Active TSS	Stomach Mucosa	stomach
37	chr6:127663600-127665600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr6:127663600-127665600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:127663600-127665600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr6:127663600-127665600	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr6:127663600-127665600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr6:127663600-127665600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr6:127663600-127665600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
44	chr6:127663600-127665600	Active TSS	Esophagus	oesophagus
45	chr6:127663600-127665600	Active TSS	Rectal Mucosa Donor 31	rectum
46	chr6:127663600-127665600	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr6:127663600-127665600	Active TSS	Small Intestine	intestine
48	chr6:127663600-127665600	Bivalent/Poised TSS	HepG2	liver
49	chr6:127663600-127665800	Active TSS	A549	lung
50	chr6:127663600-127666000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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