Variant report

Variant	rs1800949
Chromosome Location	chr6:132128564-132128565
allele	C/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	HA-E2F1	chr6:132128481-132129834	MCF-7	breast:	n/a	chr6:132129428-132129438
2	MAZ	chr6:132128209-132129880	IMR90	lung:	n/a	chr6:132128892-132128902
3	HDAC2	chr6:132128448-132129077	HepG2	liver:	n/a	chr6:132128474-132128483
4	POLR2A	chr6:132128457-132129782	H1-hESC	embryonic stem cell:	n/a	n/a
5	CREB1	chr6:132128465-132129850	HepG2	liver:	n/a	n/a
6	MAX	chr6:132128446-132129843	HepG2	liver:	n/a	chr6:132128892-132128902
7	SIN3A	chr6:132128489-132129041	H1-hESC	embryonic stem cell:	n/a	n/a
8	NFIC	chr6:132128536-132129339	ECC-1	luminal epithelium:	n/a	n/a
9	CTCF	chr6:132128520-132128670	A549	lung:	n/a	n/a
10	YY1	chr6:132128544-132129673	HepG2	liver:	n/a	chr6:132129467-132129476 chr6:132129545-132129559 chr6:132128844-132128858 chr6:132129431-132129445 chr6:132129461-132129475
11	JUND	chr6:132128511-132128939	H1-hESC	embryonic stem cell:	n/a	n/a
12	ZNF143	chr6:132128510-132128917	H1-hESC	embryonic stem cell:	n/a	n/a
13	MAX	chr6:132128503-132129175	ECC-1	luminal epithelium:	n/a	chr6:132128892-132128902
14	TAF1	chr6:132128547-132129570	H1-hESC	embryonic stem cell:	n/a	n/a
15	MXI1	chr6:132128154-132130243	IMR90	lung:	n/a	n/a
16	MAX	chr6:132128489-132129756	A549	lung:	n/a	chr6:132128892-132128902
17	MAX	chr6:132128492-132129792	HepG2	liver:	n/a	chr6:132128892-132128902
18	MAX	chr6:132128554-132129093	A549	lung:	n/a	chr6:132128892-132128902
19	CTCF	chr6:132128540-132128690	GM12864	blood:	n/a	n/a
20	RAD21	chr6:132128504-132129067	H1-hESC	embryonic stem cell:	n/a	n/a
21	E2F6	chr6:132128393-132129099	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr6:132128560-132128710	NHDF-neo	bronchial:	n/a	n/a
23	POLR2A	chr6:132128563-132129101	U87	brain:	n/a	n/a
24	TAF1	chr6:132128529-132129729	H1-hESC	embryonic stem cell:	n/a	n/a
25	MXI1	chr6:132128526-132130206	HepG2	liver:	n/a	n/a
26	NR2F2	chr6:132128508-132129136	MCF-7	breast:	n/a	n/a
27	E2F6	chr6:132128557-132128994	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:132128149..132132112-chr6:132147030..132152072,5	MCF-7	breast:
2	chr6:132127914..132130474-chr8:77911866..77914153,2	MCF-7	breast:
3	chr6:132127756..132130246-chr6:132148008..132150797,2	MCF-7	breast:
4	chr6:132126867..132133246-chr6:132138030..132146402,10	MCF-7	breast:
5	chr6:132126588..132131688-chr6:132138399..132143000,6	MCF-7	breast:

Variant related genes	Relation type
ENPP1	TF binding region
ENSG00000237115	Chromatin interaction
ENSG00000219532	Chromatin interaction
ENSG00000200895	Chromatin interaction
ENSG00000164751	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10457576	0.94[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12201710	0.94[CEU][hapmap];0.91[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6939185	0.82[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs766592	0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs7756163	0.82[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs7771841	0.82[CHB][hapmap]
rs943003	0.81[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9493103	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv515476	chr6:131615425-132228577	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv7968	chr6:131917172-132321099	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv830810	chr6:131960923-132138396	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv886670	chr6:132071193-132193395	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
5	nsv886671	chr6:132071193-132203432	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
6	nsv5479	chr6:132101897-132136593	Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
7	esv3423490	chr6:132127884-132130632	Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
8	esv3434209	chr6:132128409-132130407	Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1800949	ENPP1	cis	cerebellum	SCAN
rs1800949	CYB5R2	trans	lymphoblastoid	seeQTL
rs1800949	ENPP3	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:132128000-132128600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
2	chr6:132128000-132130400	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr6:132128200-132128600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:132128200-132128600	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
5	chr6:132128200-132128600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
6	chr6:132128200-132128600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:132128200-132128600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:132128200-132128600	Bivalent/Poised TSS	Primary T cells from cord blood	blood
9	chr6:132128200-132128600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
10	chr6:132128200-132128600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr6:132128200-132128600	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
12	chr6:132128200-132128600	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:132128200-132128600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
14	chr6:132128200-132128600	Flanking Active TSS	A549	lung
15	chr6:132128200-132128800	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr6:132128200-132128800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
17	chr6:132128200-132128800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr6:132128200-132128800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr6:132128200-132128800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:132128200-132128800	Flanking Active TSS	Adipose Nuclei	Adipose
21	chr6:132128200-132128800	Flanking Active TSS	Duodenum Mucosa	Duodenum
22	chr6:132128200-132128800	Bivalent/Poised TSS	Fetal Brain Male	brain
23	chr6:132128200-132128800	Flanking Active TSS	HSMMtube	muscle
24	chr6:132128200-132128800	Flanking Bivalent TSS/Enh	HUVEC	blood vessel
25	chr6:132128200-132128800	Flanking Active TSS	NH-A	brain
26	chr6:132128200-132128800	Flanking Active TSS	NHLF	lung
27	chr6:132128200-132128800	Flanking Active TSS	Osteobl	bone
28	chr6:132128200-132129000	Enhancers	Stomach Mucosa	stomach
29	chr6:132128200-132129400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr6:132128200-132129400	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
31	chr6:132128200-132129600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr6:132128200-132129600	Active TSS	Brain Cingulate Gyrus	brain
33	chr6:132128200-132129600	Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr6:132128200-132129800	Active TSS	Brain Angular Gyrus	brain
35	chr6:132128200-132129800	Active TSS	Brain Hippocampus Middle	brain
36	chr6:132128200-132130000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:132128200-132130000	Active TSS	Fetal Kidney	kidney
38	chr6:132128200-132130200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:132128200-132130200	Active TSS	Brain Anterior Caudate	brain
40	chr6:132128200-132130200	Active TSS	Brain Inferior Temporal Lobe	brain
41	chr6:132128200-132130200	Active TSS	Stomach Smooth Muscle	stomach
42	chr6:132128200-132130400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:132128200-132130800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:132128400-132128600	Flanking Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr6:132128400-132128600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr6:132128400-132128600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
47	chr6:132128400-132128600	Bivalent/Poised TSS	Primary B cells from cord blood	blood
48	chr6:132128400-132128600	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
49	chr6:132128400-132128600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
50	chr6:132128400-132128600	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--

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