Variant report

Variant	rs9277965
Chromosome Location	chr6:33256397-33256398
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:24)
CpG islands
(count:61)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:24 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:33256326-33257887	HCT-116	colon:	n/a	chr6:33257146-33257155
2	SREBP1	chr6:33256021-33257935	GM12878	blood:	n/a	n/a
3	POLR2A	chr6:33256261-33262240	K562	blood:	n/a	n/a
4	SIN3AK20	chr6:33256365-33258220	MCF-7	breast:	n/a	n/a
5	PML	chr6:33256071-33258380	GM12878	blood:	n/a	n/a
6	SIN3AK20	chr6:33256245-33257710	PANC-1	pancreas:	n/a	n/a
7	UBTF	chr6:33256344-33256953	K562	blood:	n/a	n/a
8	ELF1	chr6:33256210-33257755	GM12878	blood:	n/a	chr6:33257330-33257339 chr6:33257364-33257377
9	NR2F2	chr6:33256376-33257919	K562	blood:	n/a	n/a
10	ELF1	chr6:33256369-33257784	GM12878	blood:	n/a	chr6:33257330-33257339 chr6:33257364-33257377
11	POLR2A	chr6:33256351-33257150	MCF-7	breast:	n/a	n/a
12	MXI1	chr6:33255495-33258553	IMR90	lung:	n/a	chr6:33257880-33257889
13	RUNX3	chr6:33256290-33257649	GM12878	blood:	n/a	n/a
14	MTA3	chr6:33256062-33258137	GM12878	blood:	n/a	n/a
15	POLR2A	chr6:33256353-33258736	HL-60	blood:	n/a	n/a
16	SIN3AK20	chr6:33256159-33257885	K562	blood:	n/a	n/a
17	MAX	chr6:33256052-33257955	K562	blood:	n/a	chr6:33257146-33257155
18	POLR2A	chr6:33256302-33256549	HepG2	liver:	n/a	n/a
19	STAT5A	chr6:33256209-33258123	GM12878	blood:	n/a	chr6:33257209-33257220
20	POLR2A	chr6:33256383-33257115	MCF-7	breast:	n/a	n/a
21	GABPA	chr6:33256083-33258317	MCF-7	breast:	n/a	chr6:33256822-33256831
22	POLR2A	chr6:33256307-33259037	K562	blood:	n/a	n/a
23	GABPA	chr6:33256258-33257976	SK-N-SH	brain:	n/a	chr6:33256822-33256831
24	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	chr6:33256377-33256427	PFSK-1	brain:	n/a
2	chr6:33256377-33256427	Hepatocyte	liver:	n/a
3	chr6:33256377-33256427	HMEC	breast:	n/a
4	chr6:33256377-33256427	Caco-2	colon:	n/a
5	chr6:33256377-33256427	AG04449	skin:	fetal
6	chr6:33256377-33256427	HRPEpiC	eye:	n/a
7	chr6:33256377-33256427	GM06990	blood:	n/a
8	chr6:33256377-33256427	HUVEC	blood vessel:	n/a
9	chr6:33256377-33256427	SK-N-MC	brain:	n/a
10	chr6:33256377-33256427	SAEC	small airway:	n/a
11	chr6:33256377-33256427	RPTEC	kidney:	n/a
12	chr6:33256377-33256427	SK-N-SH	brain:	n/a
13	chr6:33256377-33256427	ovcar-3	ovarian:	n/a
14	chr6:33256377-33256427	Hela-S3	cervix:	n/a
15	chr6:33256377-33256427	HCT-116	colon:	n/a
16	chr6:33256377-33256427	HCM	heart:	n/a
17	chr6:33256377-33256427	HL-60	blood:	n/a
18	chr6:33256377-33256427	CMK	blood:	n/a
19	chr6:33256377-33256427	AG09319	gingival:	n/a
20	chr6:33256377-33256427	NHDF-neo	bronchial:	n/a
21	chr6:33256377-33256427	NHBE	bronchial:	n/a
22	chr6:33256377-33256427	BJ	skin:	n/a
23	chr6:33256377-33256427	GM12891	blood:	n/a
24	chr6:33256377-33256427	H1-hESC	embryonic stem cell:	embryo
25	chr6:33256377-33256427	U87	brain:	n/a
26	chr6:33256377-33256427	GM12892	blood:	n/a
27	chr6:33256377-33256427	SKMC	muscle:	n/a
28	chr6:33256377-33256427	HAEpiC	amniotic membrane:	n/a
29	chr6:33256377-33256427	HCPEpiC	choroid plexus:	n/a
30	chr6:33256377-33256427	T-47D	breast:	n/a
31	chr6:33256377-33256427	ProgFib	skin:	n/a
32	chr6:33256377-33256427	Jurkat	blood:	n/a
33	chr6:33256377-33256427	HRCEpiC	kidney:	n/a
34	chr6:33256377-33256427	NH-A	brain:	n/a
35	chr6:33256377-33256427	PrEC	prostate:	n/a
36	chr6:33256377-33256427	HIPEpiC	eye:	n/a
37	chr6:33256377-33256427	HPAEpiC	pulmonary alveolar:	n/a
38	chr6:33256377-33256427	MCF-7	breast:	n/a
39	chr6:33256377-33256427	HEEpiC	esophagus:	n/a
40	chr6:33256377-33256427	MCF10A-Er-Src	breast:	n/a
41	chr6:33256377-33256427	AoSMC	blood vessel:	n/a
42	chr6:33256377-33256427	HNPCEpiC	eye:	n/a
43	chr6:33256377-33256427	IMR90	lung:	fetal
44	chr6:33256377-33256427	PANC-1	pancreas:	n/a
45	chr6:33256377-33256427	BE2_C	brain:	n/a
46	chr6:33256377-33256427	A549	lung:	n/a
47	chr6:33256377-33256427	HepG2	liver:	n/a
48	chr6:33256377-33256427	AG10803	skin:	n/a
49	chr6:33256377-33256427	NT2-D1	testis:	n/a
50	chr6:33256377-33256427	AG09309	skin:	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
PFDN6	CpG island
WDR46	CpG island
ENSG00000202538	Chromatin interaction
ENSG00000204257	Chromatin interaction
ENSG00000197283	Chromatin interaction
ENSG00000264085	Chromatin interaction
ENSG00000231925	Chromatin interaction
ENSG00000112511	Chromatin interaction
ENSG00000204256	Chromatin interaction
ENSG00000204228	Chromatin interaction
ENSG00000112514	Chromatin interaction
ENSG00000223837	Chromatin interaction
ENSG00000200795	Chromatin interaction
ENSG00000237649	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1800837	0.91[ASN][1000 genomes]
rs3445	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs458434	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs460568	0.87[EUR][1000 genomes]
rs461338	0.86[EUR][1000 genomes]
rs462618	0.86[EUR][1000 genomes]
rs464921	0.87[EUR][1000 genomes]
rs466886	0.87[EUR][1000 genomes]
rs9277956	0.84[EUR][1000 genomes]
rs9277958	0.86[EUR][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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9277965	B3GALT4	cis	multi-tissue	Pritchard
rs9277965	STK38	cis	parietal	SCAN
rs9277965	VPS52	cis	multi-tissue	Pritchard
rs9277965	B3GALT4	cis	Cerebellum	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33245800-33256400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:33255400-33256400	Weak transcription	Aorta	Aorta
3	chr6:33255400-33256400	Transcr. at gene 5' and 3'	Dnd41	blood
4	chr6:33255600-33256400	Enhancers	Placenta Amnion	Placenta Amnion
5	chr6:33255600-33257000	Flanking Active TSS	Primary hematopoietic stem cells	blood
6	chr6:33255800-33256400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
7	chr6:33255800-33256400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr6:33255800-33256400	Flanking Active TSS	GM12878-XiMat	blood
9	chr6:33255800-33256400	Transcr. at gene 5' and 3'	K562	blood
10	chr6:33255800-33256400	Transcr. at gene 5' and 3'	NHEK	skin
11	chr6:33255800-33256600	Flanking Active TSS	Primary T cells from cord blood	blood
12	chr6:33255800-33256600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:33255800-33256600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:33255800-33256600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:33255800-33256600	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr6:33255800-33256600	Flanking Active TSS	Brain Substantia Nigra	brain
17	chr6:33255800-33256600	Flanking Active TSS	Colon Smooth Muscle	Colon
18	chr6:33255800-33256600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
19	chr6:33255800-33256600	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
20	chr6:33255800-33256600	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr6:33255800-33256600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr6:33255800-33256800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr6:33255800-33256800	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr6:33255800-33257000	Flanking Active TSS	Primary B cells from cord blood	blood
25	chr6:33255800-33257800	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:33255800-33258800	Active TSS	HUES64 Cell Line	embryonic stem cell
27	chr6:33256000-33256400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr6:33256000-33256400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
29	chr6:33256000-33256400	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
30	chr6:33256000-33256400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr6:33256000-33256400	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr6:33256000-33256400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr6:33256000-33256400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
34	chr6:33256000-33256400	Flanking Active TSS	Fetal Intestine Small	intestine
35	chr6:33256000-33256400	Flanking Active TSS	Fetal Kidney	kidney
36	chr6:33256000-33256400	Flanking Active TSS	Pancreas	Pancrea
37	chr6:33256000-33256400	Flanking Active TSS	Right Ventricle	heart
38	chr6:33256000-33256400	Flanking Active TSS	Stomach Mucosa	stomach
39	chr6:33256000-33256400	Flanking Active TSS	Hela-S3	cervix
40	chr6:33256000-33256400	Flanking Active TSS	HSMM	muscle
41	chr6:33256000-33256400	Flanking Active TSS	HSMMtube	muscle
42	chr6:33256000-33256400	Flanking Active TSS	HUVEC	blood vessel
43	chr6:33256000-33256400	Flanking Active TSS	NH-A	brain
44	chr6:33256000-33256400	Transcr. at gene 5' and 3'	NHLF	lung
45	chr6:33256000-33256400	Flanking Active TSS	Osteobl	bone
46	chr6:33256000-33256600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:33256000-33256600	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:33256000-33256600	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
49	chr6:33256000-33256600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:33256000-33256600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood

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