Variant report

Variant	rs73119219
Chromosome Location	chr12:56111667-56111668
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	POLR2A	chr12:56111246-56111681	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:56109542-56111672	GM12891	blood:	n/a	n/a
3	RUNX3	chr12:56111284-56112375	GM12878	blood:	n/a	n/a
4	BCL3	chr12:56111388-56111893	GM12878	blood:	n/a	chr12:56111687-56111696 chr12:56111489-56111498
5	POLR2A	chr12:56109324-56112454	U87	brain:	n/a	n/a
6	IKZF1	chr12:56111365-56112140	GM12878	blood:	n/a	chr12:56111725-56111733
7	BATF	chr12:56111303-56111749	GM12878	blood:	n/a	chr12:56111533-56111544 chr12:56111490-56111501
8	STAT5A	chr12:56111319-56111754	GM12878	blood:	n/a	chr12:56111685-56111696
9	SPI1	chr12:56111269-56112075	GM12878	blood:	n/a	chr12:56111687-56111696 chr12:56111651-56111664
10	FOSL2	chr12:56111175-56111714	A549	lung:	n/a	chr12:56111486-56111497 chr12:56111489-56111499 chr12:56111489-56111499 chr12:56111489-56111499 chr12:56111488-56111500 chr12:56111491-56111498 chr12:56111489-56111499 chr12:56111490-56111498 chr12:56111490-56111498
11	MTA3	chr12:56109254-56112410	GM12878	blood:	n/a	n/a
12	FOS	chr12:56111320-56111685	HUVEC	blood vessel:	n/a	chr12:56111486-56111497 chr12:56111489-56111499 chr12:56111489-56111499 chr12:56111488-56111499 chr12:56111489-56111499 chr12:56111488-56111500 chr12:56111491-56111498 chr12:56111489-56111499 chr12:56111490-56111498 chr12:56111490-56111498
13	ATF2	chr12:56111249-56111934	GM12878	blood:	n/a	n/a
14	FOXM1	chr12:56111323-56112000	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:56109562-56111806	GM12878	blood:	n/a	n/a
16	MAZ	chr12:56110768-56112402	IMR90	lung:	n/a	chr12:56111489-56111498
17	NR2F2	chr12:56111157-56111720	K562	blood:	n/a	n/a
18	CUX1	chr12:56111547-56111860	GM12878	blood:	n/a	n/a
19	POLR2A	chr12:56109568-56111823	GM12878	blood:	n/a	n/a
20	PML	chr12:56109410-56111998	GM12878	blood:	n/a	chr12:56111491-56111500
21	SPI1	chr12:56111496-56111874	GM12891	blood:	n/a	chr12:56111687-56111696 chr12:56111651-56111664
22	POLR2A	chr12:56111437-56111716	HepG2	liver:	n/a	n/a
23	POLR2A	chr12:56109229-56112495	U87	brain:	n/a	n/a
24	FOS	chr12:56111310-56111670	MCF10A-Er-Src	breast:	n/a	chr12:56111486-56111497 chr12:56111489-56111499 chr12:56111489-56111499 chr12:56111488-56111499 chr12:56111489-56111499 chr12:56111488-56111500 chr12:56111491-56111498 chr12:56111489-56111499 chr12:56111490-56111498 chr12:56111490-56111498
25	TCF3	chr12:56111563-56111814	GM12878	blood:	n/a	chr12:56111631-56111646
26	ATF2	chr12:56111255-56111697	GM12878	blood:	n/a	n/a
27	MTA3	chr12:56111369-56111938	GM12878	blood:	n/a	n/a
28	SPI1	chr12:56111510-56111914	GM12891	blood:	n/a	chr12:56111687-56111696 chr12:56111651-56111664
29	TBL1XR1	chr12:56111433-56111821	GM12878	blood:	n/a	n/a
30	JUN	chr12:56110995-56111847	K562	blood:	n/a	chr12:56111486-56111497 chr12:56111489-56111499 chr12:56111489-56111499 chr12:56111489-56111499 chr12:56111488-56111500 chr12:56111491-56111498 chr12:56111489-56111499 chr12:56111490-56111498 chr12:56111490-56111498
31	TCF12	chr12:56111532-56111798	GM12878	blood:	n/a	n/a
32	NFIC	chr12:56111279-56112131	GM12878	blood:	n/a	n/a
33	EBF1	chr12:56111049-56112012	GM12878	blood:	n/a	chr12:56111282-56111292 chr12:56111672-56111682 chr12:56111671-56111682 chr12:56111670-56111683
34	RUNX3	chr12:56110841-56112374	GM12878	blood:	n/a	n/a
35	TAF1	chr12:56111287-56111674	GM12878	blood:	n/a	n/a
36	EBF1	chr12:56111007-56112247	GM12878	blood:	n/a	chr12:56111282-56111292 chr12:56111672-56111682 chr12:56111671-56111682 chr12:56111670-56111683
37	SPI1	chr12:56111535-56111891	GM12878	blood:	n/a	chr12:56111687-56111696 chr12:56111651-56111664
38	EBF1	chr12:56110962-56112251	GM12878	blood:	n/a	chr12:56111282-56111292 chr12:56111672-56111682 chr12:56111671-56111682 chr12:56111670-56111683
39	POLR2A	chr12:56109478-56111736	U87	brain:	n/a	n/a
40	STAT5A	chr12:56111434-56111986	GM12878	blood:	n/a	chr12:56111685-56111696 chr12:56111934-56111954 chr12:56111934-56111954 chr12:56111761-56111769
41	EP300	chr12:56111487-56111807	GM12878	blood:	n/a	chr12:56111489-56111498
42	SPI1	chr12:56111623-56111802	GM12878	blood:	n/a	chr12:56111687-56111696 chr12:56111651-56111664
43	TCF3	chr12:56111439-56111899	GM12878	blood:	n/a	chr12:56111631-56111646
44	POLR2A	chr12:56109033-56113048	H1-hESC	embryonic stem cell:	n/a	n/a
45	POLR2A	chr12:56109478-56111709	U87	brain:	n/a	n/a
46	TCF12	chr12:56111527-56111787	GM12878	blood:	n/a	n/a
47	EP300	chr12:56111391-56111816	GM12878	blood:	n/a	chr12:56111489-56111498

No.	Distal block	Cell Line	Cell type
1	chr12:56052433..56055295-chr12:56110184..56112176,2	MCF-7	breast:
2	chr12:56110788..56112925-chr12:56434548..56436150,2	K562	blood:
3	chr12:56073967..56077119-chr12:56108776..56115360,8	MCF-7	breast:
4	chr12:56073502..56076646-chr12:56111009..56113178,3	MCF-7	breast:
5	chr12:56107652..56112121-chr12:56134921..56139203,6	MCF-7	breast:

Variant related genes	Relation type
RDH5	TF binding region
ITGA7	TF binding region
ENSG00000257449	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000258921	Chromatin interaction
ENSG00000170439	Chromatin interaction
ENSG00000197728	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs2231464	0.84[AMR][1000 genomes]
rs4457792	0.91[EUR][1000 genomes]
rs73119231	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948625	chr12:55838718-56118833	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv525231	chr12:56076919-56124332	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
4	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs73119219	ENSG00000135441	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56109000-56115600	Flanking Active TSS	Stomach Smooth Muscle	stomach
2	chr12:56109200-56112200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
3	chr12:56109400-56112400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
4	chr12:56110000-56113000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:56110200-56112400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr12:56110400-56111800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
7	chr12:56110400-56111800	Flanking Active TSS	Rectal Smooth Muscle	rectum
8	chr12:56110400-56111800	Flanking Active TSS	Hela-S3	cervix
9	chr12:56110400-56112000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:56110400-56112000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr12:56110400-56112600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr12:56110400-56112600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
13	chr12:56110400-56112600	Flanking Active TSS	Osteobl	bone
14	chr12:56110600-56111800	Enhancers	Spleen	Spleen
15	chr12:56110600-56111800	Flanking Active TSS	Dnd41	blood
16	chr12:56110600-56111800	Flanking Active TSS	NHDF-Ad	bronchial
17	chr12:56110600-56111800	Flanking Active TSS	NHLF	lung
18	chr12:56110600-56112000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr12:56110600-56112000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:56110600-56112200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr12:56110600-56112600	Flanking Active TSS	Colon Smooth Muscle	Colon
22	chr12:56110600-56112800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:56110600-56113000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr12:56110600-56113000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:56110600-56113000	Flanking Active TSS	GM12878-XiMat	blood
26	chr12:56110600-56113600	Flanking Active TSS	HSMMtube	muscle
27	chr12:56110800-56111800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:56110800-56111800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr12:56110800-56111800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr12:56110800-56111800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr12:56110800-56112000	Enhancers	Primary hematopoietic stem cells	blood
32	chr12:56110800-56112000	Flanking Active TSS	Colonic Mucosa	Colon
33	chr12:56110800-56112600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr12:56110800-56112600	Enhancers	Primary B cells from peripheral blood	blood
35	chr12:56110800-56112600	Enhancers	Placenta	Placenta
36	chr12:56110800-56112600	Enhancers	Small Intestine	intestine
37	chr12:56110800-56113000	Enhancers	Fetal Heart	heart
38	chr12:56110800-56113200	Enhancers	Ovary	ovary
39	chr12:56110800-56114600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr12:56111000-56111800	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
41	chr12:56111000-56111800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:56111000-56112200	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr12:56111000-56112200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:56111000-56112400	Enhancers	Primary T cells fromperipheralblood	blood
45	chr12:56111000-56112400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
46	chr12:56111000-56112400	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr12:56111000-56112400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr12:56111000-56112600	Enhancers	Fetal Intestine Large	intestine
49	chr12:56111000-56112800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:56111000-56114200	Enhancers	Psoas Muscle	Psoas

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