Variant report

Variant	rs239936
Chromosome Location	chr6:167411616-167411617
allele	A/G
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	MXI1	chr6:167410690-167413888	SK-N-SH	brain:	n/a	n/a
2	MTA3	chr6:167411093-167411710	GM12878	blood:	n/a	n/a
3	CTCF	chr6:167411158-167411732	GM12878	blood:	n/a	n/a
4	ZBTB7A	chr6:167411317-167411900	K562	blood:	n/a	n/a
5	YY1	chr6:167411212-167411691	GM12892	blood:	n/a	chr6:167411607-167411618 chr6:167411642-167411656
6	CTCF	chr6:167411019-167411693	SK-N-SH	brain:	n/a	n/a
7	E2F6	chr6:167411056-167413529	K562	blood:	n/a	chr6:167412658-167412667 chr6:167412069-167412078 chr6:167412074-167412084 chr6:167411948-167411958 chr6:167412750-167412759 chr6:167411611-167411621
8	POLR2A	chr6:167411008-167413402	K562	blood:	n/a	n/a
9	MAX	chr6:167410910-167413570	K562	blood:	n/a	chr6:167411336-167411346 chr6:167411672-167411681
10	ELF1	chr6:167411123-167413415	GM12878	blood:	n/a	chr6:167412291-167412300 chr6:167412289-167412302 chr6:167413015-167413027 chr6:167412290-167412301
11	MXI1	chr6:167411099-167413123	Hela-S3	cervix:	n/a	n/a
12	SIN3A	chr6:167411180-167413573	H1-hESC	embryonic stem cell:	n/a	chr6:167412660-167412673 chr6:167412702-167412715
13	EGR1	chr6:167411213-167411638	MCF-7	breast:	n/a	n/a
14	MAX	chr6:167411062-167411873	ECC-1	luminal epithelium:	n/a	chr6:167411336-167411346 chr6:167411672-167411681
15	ETS1	chr6:167411083-167411630	K562	blood:	n/a	n/a
16	HCFC1	chr6:167411205-167411673	K562	blood:	n/a	n/a
17	POLR2A	chr6:167411506-167411671	Gliobla	brain:	n/a	n/a
18	MYC	chr6:167411148-167411907	NB4	blood:	n/a	chr6:167411336-167411346 chr6:167411672-167411681
19	MAX	chr6:167411143-167411980	H1-hESC	embryonic stem cell:	n/a	chr6:167411336-167411346 chr6:167411672-167411681
20	SMARCB1	chr6:167411134-167413490	Hela-S3	cervix:	n/a	n/a
21	MYC	chr6:167411170-167411650	MCF10A-Er-Src	breast:	n/a	chr6:167411336-167411346
22	MAX	chr6:167411077-167411763	HCT-116	colon:	n/a	chr6:167411336-167411346 chr6:167411672-167411681
23	PML	chr6:167411211-167411654	K562	blood:	n/a	n/a
24	POLR2A	chr6:167411595-167413616	Raji	blood:	n/a	n/a
25	RAD21	chr6:167411139-167411634	GM12878	blood:	n/a	n/a
26	RAD21	chr6:167411231-167411621	SK-N-SH_RA	brain:	n/a	n/a
27	E2F4	chr6:167410844-167413816	MCF10A-Er-Src	breast:	n/a	chr6:167412658-167412667 chr6:167412069-167412078 chr6:167412074-167412084 chr6:167411948-167411958 chr6:167412750-167412759 chr6:167411611-167411621
28	RAD21	chr6:167411198-167411650	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr6:167411141-167411692	MCF-7	breast:	n/a	chr6:167411336-167411346 chr6:167411672-167411681
30	MAX	chr6:167411209-167411990	Hela-S3	cervix:	n/a	chr6:167411336-167411346 chr6:167411672-167411681
31	MYC	chr6:167411131-167413550	K562	blood:	n/a	chr6:167411336-167411346 chr6:167411672-167411681
32	SIN3AK20	chr6:167411152-167411689	PFSK-1	brain:	n/a	n/a
33	RCOR1	chr6:167411127-167411686	Hela-S3	cervix:	n/a	n/a
34	CTCF	chr6:167411302-167411656	MCF-7	breast:	n/a	n/a
35	CTCF	chr6:167411605-167411637	GM12891	blood:	n/a	n/a
36	SMC3	chr6:167411143-167411917	GM12878	blood:	n/a	n/a
37	POLR2A	chr6:167411046-167411664	K562	blood:	n/a	n/a
38	RUNX3	chr6:167410991-167411649	GM12878	blood:	n/a	n/a
39	YY1	chr6:167411239-167411665	GM12878	blood:	n/a	chr6:167411607-167411618 chr6:167411642-167411656
40	ELF1	chr6:167411532-167413073	K562	blood:	n/a	chr6:167412291-167412300 chr6:167412289-167412302 chr6:167413015-167413027 chr6:167412290-167412301
41	MAX	chr6:167411173-167411815	K562	blood:	n/a	chr6:167411336-167411346 chr6:167411672-167411681
42	CTCF	chr6:167411262-167411774	K562	blood:	n/a	n/a
43	POLR2A	chr6:167411078-167413097	IMR90	lung:	n/a	n/a
44	POLR2A	chr6:167411099-167411662	GM12878	blood:	n/a	n/a
45	MAX	chr6:167411065-167411858	A549	lung:	n/a	chr6:167411336-167411346 chr6:167411672-167411681
46	CBX3	chr6:167411106-167411749	K562	blood:	n/a	n/a
47	POLR2A	chr6:167411265-167411668	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr6:167411011-167413472	Hela-S3	cervix:	n/a	n/a
49	E2F6	chr6:167411233-167412999	K562	blood:	n/a	chr6:167412658-167412667 chr6:167412069-167412078 chr6:167412074-167412084 chr6:167411948-167411958 chr6:167412750-167412759 chr6:167411611-167411621
50	CTCF	chr6:167411573-167411654	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:167368436..167372370-chr6:167409956..167415121,7	MCF-7	breast:
2	chr6:167410797..167412644-chr6:167437633..167439150,2	MCF-7	breast:
3	chr6:167353766..167357800-chr6:167411292..167413274,3	K562	blood:
4	chr6:167368335..167372073-chr6:167409735..167414257,6	K562	blood:
5	chr6:167370155..167372073-chr6:167409744..167411701,2	K562	blood:
6	chr6:167368539..167373039-chr6:167409933..167412837,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272980	TF binding region
MIR3939	TF binding region
FGFR1OP	TF binding region
ENSG00000026297	Chromatin interaction
ENSG00000213066	Chromatin interaction
ENSG00000249141	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10946198	0.80[EUR][1000 genomes]
rs10946199	0.80[EUR][1000 genomes]
rs1743440	0.80[EUR][1000 genomes]
rs1794693	0.80[EUR][1000 genomes]
rs1794694	0.80[EUR][1000 genomes]
rs376097	0.80[EUR][1000 genomes]
rs377232	0.80[EUR][1000 genomes]
rs387733	0.80[EUR][1000 genomes]
rs388406	0.80[EUR][1000 genomes]
rs400176	0.80[EUR][1000 genomes]
rs400837	0.80[EUR][1000 genomes]
rs402191	0.80[EUR][1000 genomes]
rs406095	0.80[EUR][1000 genomes]
rs407515	0.80[EUR][1000 genomes]
rs409356	0.80[EUR][1000 genomes]
rs415842	0.80[EUR][1000 genomes]
rs415890	0.80[EUR][1000 genomes]
rs416131	0.80[EUR][1000 genomes]
rs422562	0.80[EUR][1000 genomes]
rs422780	0.80[EUR][1000 genomes]
rs424185	0.80[EUR][1000 genomes]
rs430097	0.80[EUR][1000 genomes]
rs430145	0.80[EUR][1000 genomes]
rs447042	0.80[EUR][1000 genomes]
rs4710161	0.80[EUR][1000 genomes]
rs932644	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv605260	chr6:166984094-167455139	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1019381	chr6:167090236-167558598	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
3	nsv538541	chr6:167090236-167558598	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer 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	14 gene(s)	inside rSNPs	diseases
4	nsv948634	chr6:167200671-167838993	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
5	nsv482507	chr6:167282376-167474915	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
6	nsv532074	chr6:167320656-167781977	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1031039	chr6:167324021-167741439	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
8	nsv538543	chr6:167324021-167741439	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv1026972	chr6:167335031-167671042	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
10	esv3420572	chr6:167409162-167413360	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs239936	RNASET2	cis	Skin Sun Exposed Lower leg	GTEx
rs239936	AL133458.1	cis	Whole Blood	GTEx
rs239936	RNASET2	cis	Whole Blood	GTEx
rs239936	AL133458.1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:167410800-167412000	Transcr. at gene 5' and 3'	Dnd41	blood
2	chr6:167410800-167412400	Flanking Active TSS	Primary B cells from cord blood	blood
3	chr6:167411000-167412400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr6:167411000-167412400	Flanking Active TSS	Liver	Liver
5	chr6:167411000-167413800	Active TSS	Fetal Brain Female	brain
6	chr6:167411000-167414000	Active TSS	Hela-S3	cervix
7	chr6:167411200-167411800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr6:167411200-167412000	Active TSS	Placenta Amnion	Placenta Amnion
9	chr6:167411200-167412000	Active TSS	Right Atrium	heart
10	chr6:167411200-167412200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr6:167411200-167412200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
12	chr6:167411200-167412400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr6:167411200-167412400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
14	chr6:167411200-167412400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr6:167411200-167412400	Flanking Active TSS	Adipose Nuclei	Adipose
16	chr6:167411200-167413600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:167411200-167413600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr6:167411200-167413800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr6:167411200-167413800	Active TSS	HSMMtube	muscle
20	chr6:167411200-167414000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr6:167411200-167414200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:167411400-167411800	Active TSS	Primary hematopoietic stem cells	blood
23	chr6:167411400-167412000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr6:167411400-167412000	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
25	chr6:167411400-167412000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr6:167411400-167413000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr6:167411400-167413400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:167411400-167413400	Active TSS	Colon Smooth Muscle	Colon
29	chr6:167411400-167413400	Active TSS	HUVEC	blood vessel
30	chr6:167411400-167413600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
31	chr6:167411400-167413600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:167411400-167413600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:167411400-167413600	Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr6:167411400-167413600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:167411400-167413600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:167411400-167413600	Active TSS	Primary T helper cells PMA-I stimulated	--
37	chr6:167411400-167413600	Active TSS	Muscle Satellite Cultured Cells	--
38	chr6:167411400-167413600	Active TSS	Aorta	Aorta
39	chr6:167411400-167413600	Active TSS	Brain Substantia Nigra	brain
40	chr6:167411400-167413600	Active TSS	Fetal Kidney	kidney
41	chr6:167411400-167413600	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr6:167411400-167413600	Active TSS	Fetal Stomach	stomach
43	chr6:167411400-167413600	Active TSS	Left Ventricle	heart
44	chr6:167411400-167413600	Active TSS	Lung	lung
45	chr6:167411400-167413600	Active TSS	Ovary	ovary
46	chr6:167411400-167413600	Active TSS	Right Ventricle	heart
47	chr6:167411400-167413600	Active TSS	Small Intestine	intestine
48	chr6:167411400-167413600	Active TSS	Osteobl	bone
49	chr6:167411400-167413800	Active TSS	H9 Cell Line	embryonic stem cell
50	chr6:167411400-167413800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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