Variant report

Variant	rs34852409
Chromosome Location	chr3:42641851-42641852
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:450)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:450 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr3:42641512-42642402	GM12878	blood:	n/a	n/a
2	BHLHE40	chr3:42641481-42642847	K562	blood:	n/a	n/a
3	ZBTB33	chr3:42641502-42642443	HepG2	liver:	n/a	n/a
4	SETDB1	chr3:42641633-42642024	U2OS	brain:	n/a	chr3:42641918-42641927
5	NANOG	chr3:42641771-42642229	H1-hESC	embryonic stem cell:	n/a	n/a
6	TAF1	chr3:42641582-42642991	H1-neurons	neurons:	n/a	n/a
7	YY1	chr3:42641655-42642888	K562	blood:	n/a	n/a
8	YY1	chr3:42641655-42642196	SK-N-SH_RA	brain:	n/a	n/a
9	MAX	chr3:42641527-42642990	Hela-S3	cervix:	n/a	n/a
10	ELK1	chr3:42641393-42642318	GM12878	blood:	n/a	n/a
11	MYC	chr3:42641642-42642837	K562	blood:	n/a	n/a
12	ZBTB7A	chr3:42641850-42642872	K562	blood:	n/a	n/a
13	NFYB	chr3:42641741-42642189	GM12878	blood:	n/a	n/a
14	WRNIP1	chr3:42641621-42642192	GM12878	blood:	n/a	n/a
15	E2F6	chr3:42641592-42642621	H1-hESC	embryonic stem cell:	n/a	chr3:42642320-42642332 chr3:42641918-42641927 chr3:42642321-42642332
16	TAF1	chr3:42641523-42643011	H1-hESC	embryonic stem cell:	n/a	n/a
17	MAX	chr3:42641595-42642858	A549	lung:	n/a	n/a
18	HEY1	chr3:42641533-42642927	K562	blood:	n/a	n/a
19	ZNF143	chr3:42641630-42643068	Hela-S3	cervix:	n/a	n/a
20	SIN3A	chr3:42641367-42643156	H1-hESC	embryonic stem cell:	n/a	n/a
21	EBF1	chr3:42641667-42642243	GM12878	blood:	n/a	n/a
22	RCOR1	chr3:42641684-42642372	HepG2	liver:	n/a	n/a
23	TEAD4	chr3:42641677-42642281	HepG2	liver:	n/a	n/a
24	POLR2A	chr3:42641539-42642959	GM15510	blood:	n/a	n/a
25	GTF2B	chr3:42641678-42642852	K562	blood:	n/a	n/a
26	ZBTB33	chr3:42641520-42642695	HCT-116	colon:	n/a	n/a
27	TEAD4	chr3:42641820-42642327	H1-hESC	embryonic stem cell:	n/a	n/a
28	FOXP2	chr3:42641812-42642425	PFSK-1	brain:	n/a	n/a
29	POLR2A	chr3:42641414-42642833	HepG2	liver:	n/a	n/a
30	POLR2A	chr3:42641593-42644059	K562	blood:	n/a	n/a
31	SP4	chr3:42641451-42642319	H1-hESC	embryonic stem cell:	n/a	n/a
32	POLR2A	chr3:42641498-42642793	ECC-1	luminal epithelium:	n/a	n/a
33	NFYB	chr3:42641719-42642160	Hela-S3	cervix:	n/a	n/a
34	SMC3	chr3:42641487-42642965	Hela-S3	cervix:	n/a	n/a
35	HA-E2F1	chr3:42640886-42642367	MCF-7	breast:	n/a	chr3:42642320-42642332 chr3:42641918-42641927
36	STAT1	chr3:42641655-42642336	GM12878	blood:	n/a	chr3:42642321-42642333
37	TAF1	chr3:42641553-42642910	HepG2	liver:	n/a	n/a
38	NR3C1	chr3:42641845-42642479	A549	lung:	n/a	n/a
39	POLR2A	chr3:42641403-42642884	HUVEC	blood vessel:	n/a	n/a
40	EP300	chr3:42641558-42642294	GM12878	blood:	n/a	n/a
41	ZBTB33	chr3:42641722-42642281	HepG2	liver:	n/a	n/a
42	E2F6	chr3:42641621-42642947	K562	blood:	n/a	chr3:42642320-42642332 chr3:42641918-42641927 chr3:42642321-42642332
43	ELF1	chr3:42641649-42642208	MCF-7	breast:	n/a	n/a
44	MAFK	chr3:42641223-42642307	Hela-S3	cervix:	n/a	n/a
45	PML	chr3:42641354-42643034	K562	blood:	n/a	n/a
46	POLR2A	chr3:42641620-42641993	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr3:42641617-42642752	HepG2	liver:	n/a	n/a
48	TAF1	chr3:42641604-42642373	GM12878	blood:	n/a	n/a
49	CTCF	chr3:42641841-42641961	Lung_OC	lung:	n/a	n/a
50	YY1	chr3:42641763-42642762	GM12892	blood:	n/a	n/a

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:62223147..62223727-chr3:42641596..42642594,2	Hela-S3	cervix:
2	chr15:85259297..85260034-chr3:42641537..42642490,2	Hela-S3	cervix:
3	chr3:42629943..42634676-chr3:42635408..42643782,10	MCF-7	breast:
4	chr2:85132538..85133319-chr3:42641468..42642648,3	Hela-S3	cervix:
5	chr3:42640361..42643591-chr3:42693270..42696162,5	K562	blood:
6	chr3:42509273..42511295-chr3:42641295..42643446,2	MCF-7	breast:
7	chr3:42604560..42606277-chr3:42641170..42643967,2	K562	blood:
8	chr3:42640678..42643591-chr3:42694568..42696079,2	K562	blood:
9	chr3:42641420..42642298-chr8:144952427..144952949,2	HCT-116	colon:
10	chr3:42621283..42625330-chr3:42639303..42643596,7	MCF-7	breast:
11	chr16:75589583..75590159-chr3:42641596..42642441,2	Hela-S3	cervix:
12	chr3:42622208..42623993-chr3:42640628..42642693,2	MCF-7	breast:
13	chr3:42641686..42642395-chr3:105587711..105588497,2	Hela-S3	cervix:
14	chr3:42639395..42643636-chr3:42699754..42702498,4	K562	blood:
15	chr19:58694266..58695104-chr3:42641451..42642305,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
NKTR	TF binding region
ENSG00000235787	Chromatin interaction
ENSG00000008324	Chromatin interaction
ENSG00000034510	Chromatin interaction
ENSG00000230084	Chromatin interaction
ENSG00000266402	Chromatin interaction
ENSG00000171606	Chromatin interaction
ENSG00000227184	Chromatin interaction
ENSG00000114853	Chromatin interaction
ENSG00000205084	Chromatin interaction
ENSG00000093183	Chromatin interaction
ENSG00000114423	Chromatin interaction
ENSG00000140612	Chromatin interaction
ENSG00000199753	Chromatin interaction

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs1062051	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13067987	0.81[EUR][1000 genomes]
rs13072295	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13085695	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13089845	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13090902	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13093680	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13095447	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17074602	0.81[ASN][1000 genomes]
rs17074662	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17074664	0.90[ASN][1000 genomes]
rs17074669	0.90[ASN][1000 genomes]
rs17074673	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17074674	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17074680	0.90[ASN][1000 genomes]
rs17074693	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2241542	0.81[ASN][1000 genomes]
rs2271182	0.82[ASN][1000 genomes]
rs2284303	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2284304	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2300057	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2300058	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2302352	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs33969824	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs33984028	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34683820	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34687113	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34762478	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34801786	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34977988	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35216140	0.82[EUR][1000 genomes]
rs35506005	0.82[ASN][1000 genomes]
rs35676838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35770315	0.90[ASN][1000 genomes]
rs35871059	0.82[EUR][1000 genomes]
rs35890296	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36033201	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36043081	0.82[EUR][1000 genomes]
rs3774401	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3774402	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3774404	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3774406	0.82[ASN][1000 genomes]
rs3774407	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3821836	0.90[ASN][1000 genomes]
rs3846058	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3846059	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3856737	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3886782	0.95[ASN][1000 genomes]
rs3900780	0.81[EUR][1000 genomes]
rs56047094	0.82[EUR][1000 genomes]
rs56797870	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57259216	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58868911	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59914338	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60232916	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60348477	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60535002	0.82[EUR][1000 genomes]
rs61149998	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6441928	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs66786953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67059259	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67165547	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67533173	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs67583158	0.82[EUR][1000 genomes]
rs6771105	0.82[EUR][1000 genomes]
rs6772312	0.94[ASN][1000 genomes]
rs6778982	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6782164	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67832425	0.82[EUR][1000 genomes]
rs6788548	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6790204	0.81[EUR][1000 genomes]
rs6793186	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6795296	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6797491	0.82[EUR][1000 genomes]
rs68004576	0.82[EUR][1000 genomes]
rs68028490	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68071013	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72864072	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73829255	0.82[EUR][1000 genomes]
rs7617403	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7617736	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7623867	0.81[EUR][1000 genomes]
rs7624628	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3404290	chr3:42638948-42643146	Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 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	chr3:42640800-42643600	Active TSS	Hela-S3	cervix
2	chr3:42640800-42643800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:42641000-42642200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:42641000-42643400	Active TSS	Breast Myoepithelial Primary Cells	Breast
5	chr3:42641000-42643600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr3:42641200-42642000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:42641200-42642000	ZNF genes & repeats	Fetal Brain Male	brain
8	chr3:42641200-42642200	Active TSS	Brain Germinal Matrix	brain
9	chr3:42641200-42642800	Active TSS	Brain Hippocampus Middle	brain
10	chr3:42641200-42642800	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr3:42641200-42642800	Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr3:42641200-42643000	Active TSS	Liver	Liver
13	chr3:42641200-42643000	Active TSS	Brain Angular Gyrus	brain
14	chr3:42641200-42643000	Active TSS	Brain Substantia Nigra	brain
15	chr3:42641200-42643000	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr3:42641200-42643000	Active TSS	Stomach Smooth Muscle	stomach
17	chr3:42641200-42643000	Active TSS	NHEK	skin
18	chr3:42641200-42643000	Active TSS	Osteobl	bone
19	chr3:42641200-42643200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr3:42641200-42643200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:42641200-42643200	Active TSS	Fetal Lung	lung
22	chr3:42641200-42643200	Active TSS	Placenta	Placenta
23	chr3:42641200-42643400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr3:42641200-42643400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
25	chr3:42641200-42643400	Active TSS	Muscle Satellite Cultured Cells	--
26	chr3:42641200-42643400	Active TSS	Fetal Brain Female	brain
27	chr3:42641200-42643400	Active TSS	Fetal Kidney	kidney
28	chr3:42641200-42643400	Active TSS	Fetal Muscle Leg	muscle
29	chr3:42641200-42643400	Active TSS	Fetal Stomach	stomach
30	chr3:42641200-42643400	Active TSS	Fetal Thymus	thymus
31	chr3:42641200-42643400	Active TSS	Placenta Amnion	Placenta Amnion
32	chr3:42641200-42643600	Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr3:42641200-42643600	Active TSS	HUES64 Cell Line	embryonic stem cell
34	chr3:42641200-42643600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:42641200-42643600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr3:42641200-42643600	Active TSS	Fetal Intestine Large	intestine
37	chr3:42641200-42643600	Active TSS	Fetal Muscle Trunk	muscle
38	chr3:42641200-42643600	Active TSS	K562	blood
39	chr3:42641200-42643800	Active TSS	H1 Cell Line	embryonic stem cell
40	chr3:42641200-42643800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:42641200-42643800	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr3:42641200-42643800	Active TSS	iPS-20b Cell Line	embryonic stem cell
43	chr3:42641200-42643800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr3:42641200-42643800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr3:42641200-42643800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr3:42641200-42643800	Active TSS	Fetal Intestine Small	intestine
47	chr3:42641200-42643800	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr3:42641200-42643800	Active TSS	A549	lung
49	chr3:42641200-42643800	Active TSS	HSMMtube	muscle
50	chr3:42641200-42643800	Active TSS	NHLF	lung

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