Variant report

Variant	rs71459907
Chromosome Location	chr12:4648610-4648611
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	JUND	chr12:4647483-4648918	K562	blood:	n/a	chr12:4648833-4648841 chr12:4648832-4648842 chr12:4648834-4648841 chr12:4648831-4648842 chr12:4648833-4648841
2	GATA3	chr12:4648550-4648678	SH-SY5Y	brain:	n/a	n/a
3	SIN3A	chr12:4647378-4648745	GM12878	blood:	n/a	n/a
4	POLR2A	chr12:4648444-4648654	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:4647318-4648634	Hela-S3	cervix:	n/a	n/a
6	HCFC1	chr12:4646942-4648718	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:4647200-4648648	H1-hESC	embryonic stem cell:	n/a	n/a
8	E2F4	chr12:4647076-4648805	MCF10A-Er-Src	breast:	n/a	chr12:4647923-4647935 chr12:4647953-4647962 chr12:4648032-4648043
9	FOS	chr12:4648365-4648997	MCF10A-Er-Src	breast:	n/a	chr12:4648833-4648841 chr12:4648832-4648842 chr12:4648834-4648841 chr12:4648831-4648842 chr12:4648833-4648841
10	CUX1	chr12:4647299-4648724	K562	blood:	n/a	n/a
11	POLR2A	chr12:4647228-4648811	PBDE	blood:	n/a	n/a
12	EP300	chr12:4648530-4648651	GM12878	blood:	n/a	n/a
13	BRCA1	chr12:4647424-4648673	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:4648277..4650261-chr12:4658631..4661516,2	K562	blood:
2	chr12:4647147..4649763-chr12:4649895..4651987,2	MCF-7	breast:
3	chr12:4638037..4640518-chr12:4647266..4649269,3	K562	blood:

Variant related genes	Relation type
C12orf4	TF binding region
RAD51AP1	TF binding region
ENSG00000111247	Chromatin interaction
ENSG00000047621	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10492053	0.88[AFR][1000 genomes]
rs12818485	1.00[ASN][1000 genomes]
rs12831479	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16931447	1.00[ASN][1000 genomes]
rs2909376	1.00[ASN][1000 genomes]
rs2970831	1.00[ASN][1000 genomes]
rs2970832	1.00[ASN][1000 genomes]
rs2970833	1.00[ASN][1000 genomes]
rs35467270	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35711623	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35924298	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56857065	0.81[AFR][1000 genomes]
rs57308816	0.83[AFR][1000 genomes]
rs71459908	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71459911	1.00[ASN][1000 genomes]
rs7296957	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302664	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74061919	0.81[AFR][1000 genomes]
rs74061923	0.81[AFR][1000 genomes]
rs7955370	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7962626	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv557123	chr12:4436632-4736569	Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv1038332	chr12:4627992-4689300	Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv541362	chr12:4627992-4689300	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:4646400-4648800	Active TSS	HUES48 Cell Line	embryonic stem cell
2	chr12:4646400-4648800	Active TSS	iPS-20b Cell Line	embryonic stem cell
3	chr12:4646600-4648800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr12:4646600-4648800	Active TSS	Brain Angular Gyrus	brain
5	chr12:4646600-4648800	Active TSS	Hela-S3	cervix
6	chr12:4646600-4648800	Active TSS	NHDF-Ad	bronchial
7	chr12:4646600-4650000	Active TSS	K562	blood
8	chr12:4646800-4648800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr12:4646800-4648800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:4646800-4648800	Active TSS	GM12878-XiMat	blood
11	chr12:4646800-4648800	Active TSS	NHEK	skin
12	chr12:4646800-4649000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr12:4646800-4649000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr12:4646800-4649000	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr12:4646800-4649000	Active TSS	A549	lung
16	chr12:4646800-4649400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr12:4646800-4649400	Active TSS	HSMM	muscle
18	chr12:4646800-4649600	Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr12:4646800-4649600	Active TSS	NHLF	lung
20	chr12:4647000-4648800	Active TSS	HUES64 Cell Line	embryonic stem cell
21	chr12:4647000-4648800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:4647000-4648800	Active TSS	iPS-18 Cell Line	embryonic stem cell
23	chr12:4647000-4648800	Active TSS	Brain Inferior Temporal Lobe	brain
24	chr12:4647000-4649000	Active TSS	iPS-15b Cell Line	embryonic stem cell
25	chr12:4647000-4649000	Active TSS	Placenta	Placenta
26	chr12:4647000-4649200	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr12:4647000-4649400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr12:4647000-4649400	Active TSS	Fetal Intestine Large	intestine
29	chr12:4647000-4649600	Active TSS	H1 Cell Line	embryonic stem cell
30	chr12:4647000-4649600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:4647200-4648800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr12:4647200-4648800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr12:4647200-4648800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:4647200-4648800	Active TSS	H9 Cell Line	embryonic stem cell
35	chr12:4647200-4648800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr12:4647200-4648800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
37	chr12:4647200-4648800	Active TSS	Dnd41	blood
38	chr12:4647200-4649000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:4647200-4649200	Active TSS	Fetal Brain Female	brain
40	chr12:4647200-4649200	Active TSS	Fetal Muscle Trunk	muscle
41	chr12:4648000-4649000	Flanking Active TSS	Primary hematopoietic stem cells	blood
42	chr12:4648000-4649400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr12:4648000-4649600	Flanking Active TSS	HUVEC	blood vessel
44	chr12:4648200-4648800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr12:4648200-4648800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr12:4648200-4648800	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr12:4648200-4648800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr12:4648200-4648800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
49	chr12:4648200-4649000	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr12:4648200-4649000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood

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