Variant report

Variant	rs3130257
Chromosome Location	chr6:33256471-33256472
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:37)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:37 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:33256426-33257846	MCF-7	breast:	n/a	chr6:33257146-33257155
2	HCFC1	chr6:33256430-33258129	Hela-S3	cervix:	n/a	n/a
3	ZMIZ1	chr6:33256406-33257794	K562	blood:	n/a	n/a
4	MAX	chr6:33256326-33257887	HCT-116	colon:	n/a	chr6:33257146-33257155
5	SREBP1	chr6:33256021-33257935	GM12878	blood:	n/a	n/a
6	POLR2A	chr6:33256261-33262240	K562	blood:	n/a	n/a
7	SIN3AK20	chr6:33256365-33258220	MCF-7	breast:	n/a	n/a
8	PML	chr6:33256071-33258380	GM12878	blood:	n/a	n/a
9	SIN3AK20	chr6:33256245-33257710	PANC-1	pancreas:	n/a	n/a
10	UBTF	chr6:33256344-33256953	K562	blood:	n/a	n/a
11	ELF1	chr6:33256210-33257755	GM12878	blood:	n/a	chr6:33257330-33257339 chr6:33257364-33257377
12	POLR2A	chr6:33256458-33262163	SK-N-MC	brain:	n/a	n/a
13	NR2F2	chr6:33256376-33257919	K562	blood:	n/a	n/a
14	ELF1	chr6:33256369-33257784	GM12878	blood:	n/a	chr6:33257330-33257339 chr6:33257364-33257377
15	POLR2A	chr6:33256351-33257150	MCF-7	breast:	n/a	n/a
16	MXI1	chr6:33255495-33258553	IMR90	lung:	n/a	chr6:33257880-33257889
17	ELF1	chr6:33256417-33257830	HCT-116	colon:	n/a	chr6:33257330-33257339 chr6:33257364-33257377
18	RUNX3	chr6:33256290-33257649	GM12878	blood:	n/a	n/a
19	ELF1	chr6:33256430-33257919	HCT-116	colon:	n/a	chr6:33257330-33257339 chr6:33257364-33257377
20	GABPA	chr6:33256438-33257902	A549	lung:	n/a	chr6:33256822-33256831
21	RELA	chr6:33256466-33257600	GM19193	blood:	n/a	n/a
22	MTA3	chr6:33256062-33258137	GM12878	blood:	n/a	n/a
23	POLR2A	chr6:33256353-33258736	HL-60	blood:	n/a	n/a
24	SIN3AK20	chr6:33256159-33257885	K562	blood:	n/a	n/a
25	MAX	chr6:33256052-33257955	K562	blood:	n/a	chr6:33257146-33257155
26	POLR2A	chr6:33256302-33256549	HepG2	liver:	n/a	n/a
27	POLR2A	chr6:33256454-33256564	ProgFib	skin:	n/a	n/a
28	THAP1	chr6:33256409-33257723	K562	blood:	n/a	chr6:33257074-33257098
29	STAT5A	chr6:33256209-33258123	GM12878	blood:	n/a	chr6:33257209-33257220
30	MYC	chr6:33256413-33257936	K562	blood:	n/a	chr6:33257146-33257155
31	POLR2A	chr6:33256383-33257115	MCF-7	breast:	n/a	n/a
32	GABPA	chr6:33256083-33258317	MCF-7	breast:	n/a	chr6:33256822-33256831
33	POLR2A	chr6:33256307-33259037	K562	blood:	n/a	n/a
34	GABPA	chr6:33256258-33257976	SK-N-SH	brain:	n/a	chr6:33256822-33256831
35	RUNX3	chr6:33256456-33257602	GM12878	blood:	n/a	n/a
36	MYC	chr6:33256444-33257833	K562	blood:	n/a	chr6:33257146-33257155
37	MXI1	chr6:33255835-33258847	SK-N-SH	brain:	n/a	chr6:33257880-33257889

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:33256441-33256491	GM12891	blood:	n/a
2	chr6:33256441-33256491	HRPEpiC	eye:	n/a
3	chr6:33256441-33256491	HAEpiC	amniotic membrane:	n/a
4	chr6:33256441-33256491	AG10803	skin:	n/a
5	chr6:33256441-33256491	GM06990	blood:	n/a
6	chr6:33256441-33256491	HMEC	breast:	n/a
7	chr6:33256441-33256491	HIPEpiC	eye:	n/a
8	chr6:33256441-33256491	SK-N-MC	brain:	n/a
9	chr6:33256441-33256491	Hepatocyte	liver:	n/a
10	chr6:33256441-33256491	NHDF-neo	bronchial:	n/a
11	chr6:33256441-33256491	HRCEpiC	kidney:	n/a
12	chr6:33256441-33256491	NT2-D1	testis:	n/a
13	chr6:33256441-33256491	Jurkat	blood:	n/a
14	chr6:33256441-33256491	HPAEpiC	pulmonary alveolar:	n/a
15	chr6:33256441-33256491	ECC-1	luminal epithelium:	n/a
16	chr6:33256441-33256491	BJ	skin:	n/a
17	chr6:33256441-33256491	HL-60	blood:	n/a
18	chr6:33256441-33256491	ovcar-3	ovarian:	n/a
19	chr6:33256441-33256491	PFSK-1	brain:	n/a
20	chr6:33256441-33256491	IMR90	lung:	fetal
21	chr6:33256441-33256491	U87	brain:	n/a
22	chr6:33256441-33256491	GM12892	blood:	n/a
23	chr6:33256441-33256491	MCF-7	breast:	n/a
24	chr6:33256441-33256491	SK-N-SH	brain:	n/a
25	chr6:33256441-33256491	H1-hESC	embryonic stem cell:	embryo
26	chr6:33256441-33256491	HepG2	liver:	n/a
27	chr6:33256441-33256491	AG04449	skin:	fetal
28	chr6:33256441-33256491	LNCaP	prostate:	n/a
29	chr6:33256441-33256491	PANC-1	pancreas:	n/a
30	chr6:33256441-33256491	AG09309	skin:	n/a
31	chr6:33256441-33256491	K562	blood:	n/a
32	chr6:33256441-33256491	HUVEC	blood vessel:	n/a
33	chr6:33256441-33256491	T-47D	breast:	n/a
34	chr6:33256441-33256491	PrEC	prostate:	n/a
35	chr6:33256441-33256491	GM19239	blood:	n/a
36	chr6:33256441-33256491	HRE	kidney:	n/a
37	chr6:33256441-33256491	NHBE	bronchial:	n/a
38	chr6:33256441-33256491	ProgFib	skin:	n/a
39	chr6:33256441-33256491	HEEpiC	esophagus:	n/a
40	chr6:33256441-33256491	SKMC	muscle:	n/a
41	chr6:33256441-33256491	GM12878	blood:	n/a
42	chr6:33256441-33256491	HCT-116	colon:	n/a
43	chr6:33256441-33256491	NH-A	brain:	n/a
44	chr6:33256441-33256491	Caco-2	colon:	n/a
45	chr6:33256441-33256491	A549	lung:	n/a
46	chr6:33256441-33256491	HNPCEpiC	eye:	n/a
47	chr6:33256441-33256491	MCF10A-Er-Src	breast:	n/a
48	chr6:33256441-33256491	RPTEC	kidney:	n/a
49	chr6:33256441-33256491	Hela-S3	cervix:	n/a
50	chr6:33256441-33256491	SK-N-SH_RA	brain:	n/a

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:120728485..120731088-chr6:33255818..33258567,3	MCF-7	breast:
2	chr6:33255152..33256710-chr6:33377924..33379590,2	K562	blood:
3	chr6:33255047..33257514-chr6:33384371..33386134,2	K562	blood:
4	chr6:32934202..32936578-chr6:33256185..33258696,2	K562	blood:
5	chr6:33170950..33173180-chr6:33254762..33258714,3	K562	blood:
6	chr6:33254516..33257651-chr6:33384634..33387572,3	K562	blood:
7	chr6:33256218..33259091-chr6:33279064..33284854,6	MCF-7	breast:
8	chr6:32937868..32940251-chr6:33254691..33256964,2	MCF-7	breast:
9	chr6:33255490..33258967-chr6:33375507..33378634,5	MCF-7	breast:
10	chr6:33254680..33257397-chr6:33405638..33407793,2	K562	blood:
11	chr6:33255667..33257365-chr6:33384673..33386459,3	MCF-7	breast:
12	chr6:33253660..33257073-chr6:33358023..33361324,4	K562	blood:

No data

Variant related genes	Relation type
PFDN6	TF binding region
WDR46	TF binding region
WDR46	CpG island
PFDN6	CpG island
ENSG00000204256	Chromatin interaction
ENSG00000202538	Chromatin interaction
ENSG00000237649	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000264085	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000204228	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000197283	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs1755038	1.00[ASN][1000 genomes]
rs1755040	1.00[ASN][1000 genomes]
rs210190	1.00[ASN][1000 genomes]
rs213198	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2941555	1.00[ASN][1000 genomes]
rs3106196	1.00[ASN][1000 genomes]
rs3116713	1.00[ASN][1000 genomes]
rs3119026	1.00[ASN][1000 genomes]
rs3130013	1.00[ASN][1000 genomes]
rs3130021	0.84[EUR][1000 genomes]
rs3130023	1.00[ASN][1000 genomes]
rs3130026	1.00[ASN][1000 genomes]
rs3130104	1.00[ASN][1000 genomes]
rs3130258	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3130273	1.00[ASN][1000 genomes]
rs35700288	1.00[ASN][1000 genomes]
rs36003672	1.00[ASN][1000 genomes]
rs449978	1.00[ASN][1000 genomes]
rs6910721	1.00[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	nsv462893	chr6:33142539-33256471	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv602830	chr6:33142539-33256471	Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv830634	chr6:33161217-33330745	Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	139 gene(s)	inside rSNPs	diseases
4	nsv830635	chr6:33238005-33413787	Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	129 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	chr6:33255600-33257000	Flanking Active TSS	Primary hematopoietic stem cells	blood
2	chr6:33255800-33256600	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr6:33255800-33256600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:33255800-33256600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr6:33255800-33256600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr6:33255800-33256600	Flanking Active TSS	Brain Germinal Matrix	brain
7	chr6:33255800-33256600	Flanking Active TSS	Brain Substantia Nigra	brain
8	chr6:33255800-33256600	Flanking Active TSS	Colon Smooth Muscle	Colon
9	chr6:33255800-33256600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
10	chr6:33255800-33256600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
11	chr6:33255800-33256600	Flanking Active TSS	Stomach Smooth Muscle	stomach
12	chr6:33255800-33256600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr6:33255800-33256800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr6:33255800-33256800	Flanking Active TSS	Adipose Nuclei	Adipose
15	chr6:33255800-33257000	Flanking Active TSS	Primary B cells from cord blood	blood
16	chr6:33255800-33257800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
17	chr6:33255800-33258800	Active TSS	HUES64 Cell Line	embryonic stem cell
18	chr6:33256000-33256600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:33256000-33256600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:33256000-33256600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr6:33256000-33256600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:33256000-33256600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
23	chr6:33256000-33256600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:33256000-33256600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr6:33256000-33256600	Flanking Active TSS	Brain Angular Gyrus	brain
26	chr6:33256000-33256600	Flanking Active TSS	Brain Anterior Caudate	brain
27	chr6:33256000-33256600	Flanking Active TSS	Brain Cingulate Gyrus	brain
28	chr6:33256000-33256600	Flanking Active TSS	Brain Hippocampus Middle	brain
29	chr6:33256000-33256600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr6:33256000-33256600	Flanking Active TSS	Colonic Mucosa	Colon
31	chr6:33256000-33256600	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr6:33256000-33256600	Flanking Active TSS	Fetal Brain Male	brain
33	chr6:33256000-33256600	Flanking Active TSS	Fetal Brain Female	brain
34	chr6:33256000-33256600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
35	chr6:33256000-33256600	Flanking Active TSS	Rectal Smooth Muscle	rectum
36	chr6:33256000-33256600	Flanking Active TSS	Right Atrium	heart
37	chr6:33256000-33256800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr6:33256000-33256800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr6:33256000-33256800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
40	chr6:33256000-33256800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:33256000-33256800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr6:33256000-33256800	Flanking Active TSS	Liver	Liver
43	chr6:33256000-33258000	Active TSS	Psoas Muscle	Psoas
44	chr6:33256000-33258200	Active TSS	Pancreatic Islets	Pancreatic Islet
45	chr6:33256000-33258400	Active TSS	H1 Cell Line	embryonic stem cell
46	chr6:33256000-33258400	Active TSS	H9 Cell Line	embryonic stem cell
47	chr6:33256000-33258600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr6:33256000-33258600	Active TSS	iPS-20b Cell Line	embryonic stem cell
49	chr6:33256200-33256600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr6:33256200-33256600	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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