Variant report

Variant	rs3757109
Chromosome Location	chr6:74364305-74364306
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	MYC	chr6:74363561-74364897	K562	blood:	n/a	n/a
2	ZNF143	chr6:74363467-74364325	H1-hESC	embryonic stem cell:	n/a	chr6:74363880-74363890
3	HA-E2F1	chr6:74363501-74364388	MCF-7	breast:	n/a	chr6:74363878-74363887 chr6:74363784-74363793
4	YY1	chr6:74363501-74364316	ECC-1	luminal epithelium:	n/a	chr6:74363788-74363810 chr6:74363781-74363790 chr6:74363781-74363792 chr6:74363788-74363798 chr6:74363726-74363735 chr6:74363705-74363716 chr6:74363707-74363716 chr6:74363767-74363781 chr6:74363787-74363799 chr6:74363784-74363793 chr6:74363789-74363797
5	SIN3A	chr6:74362390-74364417	H1-hESC	embryonic stem cell:	n/a	n/a
6	MYC	chr6:74363484-74364519	K562	blood:	n/a	n/a
7	MYC	chr6:74363541-74364910	MCF10A-Er-Src	breast:	n/a	n/a
8	MXI1	chr6:74362128-74364844	IMR90	lung:	n/a	n/a
9	MYC	chr6:74363650-74364913	K562	blood:	n/a	n/a
10	MEF2A	chr6:74363996-74364755	K562	blood:	n/a	n/a
11	YY1	chr6:74363200-74364406	GM12878	blood:	n/a	chr6:74363788-74363810 chr6:74363781-74363790 chr6:74363414-74363428 chr6:74363781-74363792 chr6:74363788-74363798 chr6:74363417-74363431 chr6:74363726-74363735 chr6:74363453-74363467 chr6:74363705-74363716 chr6:74363707-74363716 chr6:74363767-74363781 chr6:74363787-74363799 chr6:74363784-74363793 chr6:74363461-74363470 chr6:74363789-74363797
12	HCFC1	chr6:74363256-74365359	Hela-S3	cervix:	n/a	n/a
13	MXI1	chr6:74362158-74364581	SK-N-SH	brain:	n/a	n/a
14	HEY1	chr6:74363425-74364509	HepG2	liver:	n/a	n/a
15	TCF12	chr6:74363588-74364610	A549	lung:	n/a	n/a
16	SMARCC1	chr6:74362749-74364416	Hela-S3	cervix:	n/a	n/a
17	RCOR1	chr6:74362329-74364399	Hela-S3	cervix:	n/a	n/a
18	YY1	chr6:74363205-74364397	K562	blood:	n/a	chr6:74363788-74363810 chr6:74363781-74363790 chr6:74363414-74363428 chr6:74363781-74363792 chr6:74363788-74363798 chr6:74363417-74363431 chr6:74363726-74363735 chr6:74363453-74363467 chr6:74363705-74363716 chr6:74363707-74363716 chr6:74363767-74363781 chr6:74363787-74363799 chr6:74363784-74363793 chr6:74363461-74363470 chr6:74363789-74363797
19	POLR2A	chr6:74363450-74364416	HL-60	blood:	n/a	n/a
20	MXI1	chr6:74362811-74364330	HepG2	liver:	n/a	n/a
21	MYC	chr6:74363544-74364429	H1-hESC	embryonic stem cell:	n/a	n/a
22	SMARCB1	chr6:74362949-74364421	Hela-S3	cervix:	n/a	n/a
23	ELF1	chr6:74363685-74364387	HepG2	liver:	n/a	chr6:74363759-74363771
24	USF1	chr6:74363983-74364345	HepG2	liver:	n/a	chr6:74364144-74364155 chr6:74364169-74364180
25	GTF3C2	chr6:74362850-74364512	K562	blood:	n/a	n/a
26	POLR2A	chr6:74363482-74364306	K562	blood:	n/a	n/a
27	CEBPB	chr6:74363897-74364507	A549	lung:	n/a	chr6:74364269-74364280 chr6:74364076-74364089
28	USF2	chr6:74363916-74364341	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr6:74362940-74364357	MCF-7	breast:	n/a	n/a
30	CREB1	chr6:74362747-74364446	HepG2	liver:	n/a	n/a
31	POLR2A	chr6:74363251-74364449	H1-hESC	embryonic stem cell:	n/a	n/a
32	YY1	chr6:74363525-74364345	SK-N-SH_RA	brain:	n/a	chr6:74363788-74363810 chr6:74363781-74363790 chr6:74363781-74363792 chr6:74363788-74363798 chr6:74363726-74363735 chr6:74363705-74363716 chr6:74363707-74363716 chr6:74363767-74363781 chr6:74363787-74363799 chr6:74363784-74363793 chr6:74363789-74363797
33	E2F6	chr6:74363600-74364441	A549	lung:	n/a	chr6:74363928-74363939 chr6:74363878-74363887 chr6:74363784-74363793
34	CEBPB	chr6:74363779-74364460	K562	blood:	n/a	chr6:74364269-74364280 chr6:74364076-74364089
35	POLR2A	chr6:74363329-74364458	GM12878	blood:	n/a	n/a
36	POLR2A	chr6:74363178-74364389	PFSK-1	brain:	n/a	n/a
37	MAX	chr6:74363284-74364550	HepG2	liver:	n/a	n/a
38	MYC	chr6:74364267-74364309	K562	blood:	n/a	n/a
39	HNF4A	chr6:74362871-74364330	HepG2	liver:	n/a	chr6:74363951-74363973
40	POLR2A	chr6:74363370-74364412	HL-60	blood:	n/a	n/a
41	MAX	chr6:74363330-74364364	MCF-7	breast:	n/a	n/a
42	TEAD4	chr6:74363684-74364600	HepG2	liver:	n/a	n/a
43	PAX5	chr6:74363978-74364357	GM12878	blood:	n/a	n/a
44	JUND	chr6:74363521-74364370	K562	blood:	n/a	chr6:74363703-74363712
45	PAX5	chr6:74364035-74364379	GM12878	blood:	n/a	n/a
46	CEBPB	chr6:74363583-74364651	Hela-S3	cervix:	n/a	chr6:74364269-74364280 chr6:74364076-74364089
47	CEBPB	chr6:74363911-74364383	K562	blood:	n/a	chr6:74364269-74364280 chr6:74364076-74364089
48	POLR2A	chr6:74363446-74364924	K562	blood:	n/a	n/a
49	YY1	chr6:74363305-74364326	H1-hESC	embryonic stem cell:	n/a	chr6:74363788-74363810 chr6:74363781-74363790 chr6:74363414-74363428 chr6:74363781-74363792 chr6:74363788-74363798 chr6:74363417-74363431 chr6:74363726-74363735 chr6:74363453-74363467 chr6:74363705-74363716 chr6:74363707-74363716 chr6:74363767-74363781 chr6:74363787-74363799 chr6:74363784-74363793 chr6:74363461-74363470 chr6:74363789-74363797
50	TAF7	chr6:74363209-74364325	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:74353596..74359738-chr6:74361541..74364786,8	MCF-7	breast:
2	chr6:74170014..74172890-chr6:74363161..74365164,3	K562	blood:
3	chr6:74228702..74232744-chr6:74360665..74366385,13	MCF-7	breast:
4	chr6:74220976..74234980-chr6:74352572..74366941,62	K562	blood:
5	chr6:74169971..74171514-chr6:74363161..74365275,2	K562	blood:
6	chr6:74219718..74234750-chr6:74354945..74369231,56	K562	blood:
7	chr6:74103315..74106293-chr6:74362194..74365078,3	MCF-7	breast:
8	chr6:74363322..74365404-chr6:75950708..75953547,2	MCF-7	breast:
9	chr14:35871636..35873724-chr6:74363774..74365365,2	MCF-7	breast:
10	chr6:74228067..74234767-chr6:74357105..74365312,16	MCF-7	breast:
11	chr6:74354143..74358709-chr6:74361254..74364709,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CD109-1	chr6:74364304-74364586	XLOC_005347
2	lnc-CD109-1	chr6:74364303-74364586	NONHSAT113578

Variant related genes	Relation type
SLC17A5	TF binding region
ENSG00000119899	Chromatin interaction
ENSG00000156508	Chromatin interaction
ENSG00000229862	Chromatin interaction
ENSG00000203907	Chromatin interaction
ENSG00000112695	Chromatin interaction
ENSG00000100906	Chromatin interaction
ENSG00000080007	Chromatin interaction
ENSG00000238464	Chromatin interaction
ENSG00000135297	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10455281	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10498892	0.86[ASN][1000 genomes]
rs10943112	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943113	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10943117	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11964414	0.86[ASN][1000 genomes]
rs12189556	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12193002	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195068	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12195584	0.86[ASN][1000 genomes]
rs12196281	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12197318	0.86[ASN][1000 genomes]
rs12197927	1.00[ASN][1000 genomes]
rs12203363	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210126	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210394	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210825	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12211279	1.00[ASN][1000 genomes]
rs12212297	0.86[ASN][1000 genomes]
rs12213067	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12213868	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12214877	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12216092	1.00[ASN][1000 genomes]
rs13193629	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13202151	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13203297	0.81[ASN][1000 genomes]
rs13207999	1.00[ASN][1000 genomes]
rs13211453	1.00[ASN][1000 genomes]
rs13212809	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2351118	1.00[ASN][1000 genomes]
rs2351119	1.00[ASN][1000 genomes]
rs2351120	0.81[ASN][1000 genomes]
rs2351121	1.00[ASN][1000 genomes]
rs34342150	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34613232	1.00[ASN][1000 genomes]
rs35256309	0.86[ASN][1000 genomes]
rs35468063	1.00[ASN][1000 genomes]
rs35584640	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35659919	0.86[ASN][1000 genomes]
rs35733187	1.00[ASN][1000 genomes]
rs36131846	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3734518	1.00[ASN][1000 genomes]
rs3757111	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3799288	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4708065	1.00[ASN][1000 genomes]
rs56086551	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs59383274	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438456	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62440462	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72949387	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744053	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1017716	chr6:74173173-74401162	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
6	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
8	nsv603694	chr6:74275405-74365807	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1029927	chr6:74300496-74424355	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised 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	21 gene(s)	inside rSNPs	diseases
10	nsv1027691	chr6:74302980-74417450	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer 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	21 gene(s)	inside rSNPs	diseases
11	esv3408073	chr6:74362256-74364804	Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 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	chr6:74361800-74364400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:74361800-74364600	Active TSS	Fetal Intestine Large	intestine
3	chr6:74361800-74364800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:74361800-74364800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
5	chr6:74361800-74364800	Active TSS	K562	blood
6	chr6:74361800-74365200	Active TSS	NHDF-Ad	bronchial
7	chr6:74362000-74364400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:74362000-74364400	Active TSS	Brain Anterior Caudate	brain
9	chr6:74362000-74364400	Active TSS	Fetal Muscle Leg	muscle
10	chr6:74362000-74364600	Active TSS	ES-I3 Cell Line	embryonic stem cell
11	chr6:74362000-74364600	Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr6:74362000-74364600	Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr6:74362200-74364400	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr6:74362200-74364400	Active TSS	Primary T helper cells PMA-I stimulated	--
15	chr6:74362200-74364400	Active TSS	Fetal Intestine Small	intestine
16	chr6:74362200-74364400	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr6:74362200-74364400	Active TSS	GM12878-XiMat	blood
18	chr6:74362200-74364400	Active TSS	Hela-S3	cervix
19	chr6:74362200-74364400	Active TSS	Monocytes-CD14+_RO01746	blood
20	chr6:74362200-74364600	Active TSS	NHLF	lung
21	chr6:74362200-74364800	Active TSS	Duodenum Mucosa	Duodenum
22	chr6:74362200-74365000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr6:74362200-74365000	Active TSS	Pancreatic Islets	Pancreatic Islet
24	chr6:74362200-74365000	Active TSS	HSMMtube	muscle
25	chr6:74362400-74364400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr6:74362400-74364400	Active TSS	Muscle Satellite Cultured Cells	--
27	chr6:74362400-74364400	Active TSS	Brain Angular Gyrus	brain
28	chr6:74362400-74364400	Active TSS	Brain Cingulate Gyrus	brain
29	chr6:74362400-74364400	Active TSS	Fetal Kidney	kidney
30	chr6:74362400-74364400	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr6:74362400-74364400	Active TSS	Thymus	Thymus
32	chr6:74362400-74364400	Active TSS	HMEC	breast
33	chr6:74362400-74364600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
34	chr6:74362400-74364600	Active TSS	H1 Cell Line	embryonic stem cell
35	chr6:74362400-74364600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:74362400-74364600	Active TSS	Brain Hippocampus Middle	brain
37	chr6:74362400-74364600	Active TSS	Fetal Lung	lung
38	chr6:74362400-74364600	Active TSS	Psoas Muscle	Psoas
39	chr6:74362400-74364800	Active TSS	HUES6 Cell Line	embryonic stem cell
40	chr6:74362400-74364800	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr6:74362400-74364800	Active TSS	Right Atrium	heart
42	chr6:74362400-74364800	Active TSS	Right Ventricle	heart
43	chr6:74362400-74364800	Active TSS	Stomach Smooth Muscle	stomach
44	chr6:74362600-74364400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
45	chr6:74362600-74364400	Active TSS	Primary monocytes fromperipheralblood	blood
46	chr6:74362600-74364400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr6:74362600-74364400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr6:74362600-74364400	Active TSS	Placenta	Placenta
49	chr6:74362600-74364400	Active TSS	Fetal Stomach	stomach
50	chr6:74362600-74364600	Active TSS	H9 Cell Line	embryonic stem cell

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