Variant report

Variant	rs2258043
Chromosome Location	chr12:121451425-121451426
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	CTCF	chr12:121451168-121452086	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:121017466..121019085-chr12:121449555..121451669,2	MCF-7	breast:
2	chr12:121446939..121449086-chr12:121451348..121453290,2	MCF-7	breast:

Variant related genes	Relation type
C12orf43	TF binding region
ENSG00000157895	Chromatin interaction
ENSG00000167272	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10849829	0.82[JPT][hapmap];0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs1169279	0.96[ASN][1000 genomes]
rs1169281	0.96[ASN][1000 genomes]
rs1169299	0.96[ASN][1000 genomes]
rs1169302	0.84[CHB][hapmap];0.81[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs1169303	0.96[CEU][hapmap];0.94[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1169307	0.81[YRI][hapmap]
rs1169312	0.83[MEX][hapmap]
rs1169313	0.83[MEX][hapmap]
rs2254971	1.00[ASN][1000 genomes]
rs2258287	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2259690	0.96[ASN][1000 genomes]
rs2259693	1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2259777	0.95[ASN][1000 genomes]
rs2259816	0.83[MEX][hapmap]
rs2259883	0.82[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs2260399	0.82[JPT][hapmap];0.90[YRI][hapmap];0.82[ASN][1000 genomes]
rs2260445	0.83[ASN][1000 genomes]
rs2260446	0.83[ASN][1000 genomes]
rs2264778	0.98[ASN][1000 genomes]
rs2701180	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2701189	0.80[ASN][1000 genomes]
rs4278584	0.96[ASN][1000 genomes]
rs735396	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521928	chr12:121041728-121761800	Genic enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
2	nsv1037070	chr12:121069938-121459047	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv899559	chr12:121324727-121592689	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv899560	chr12:121371233-121560581	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv899561	chr12:121376416-121525591	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv899562	chr12:121376416-121565870	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv1037195	chr12:121408540-121470375	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	esv2758318	chr12:121415845-121584813	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	esv2759917	chr12:121415845-121584813	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
10	nsv1039216	chr12:121421701-121538491	Active TSS Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
11	nsv832531	chr12:121440495-121604232	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2258043	FLJ12448	cis	multi-tissue	Pritchard

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:121429800-121451600	Strong transcription	Rectal Mucosa Donor 29	rectum
2	chr12:121436600-121452800	Weak transcription	Fetal Heart	heart
3	chr12:121437600-121452000	Strong transcription	Fetal Stomach	stomach
4	chr12:121437600-121453000	Weak transcription	Fetal Brain Male	brain
5	chr12:121437600-121453600	Weak transcription	Right Atrium	heart
6	chr12:121438600-121451600	Strong transcription	Primary T cells from cord blood	blood
7	chr12:121438600-121451800	Strong transcription	Fetal Muscle Trunk	muscle
8	chr12:121438800-121451600	Strong transcription	Stomach Smooth Muscle	stomach
9	chr12:121438800-121451800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:121438800-121451800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr12:121438800-121451800	Strong transcription	Fetal Brain Female	brain
12	chr12:121439000-121451600	Strong transcription	Brain Inferior Temporal Lobe	brain
13	chr12:121439000-121451800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:121439200-121451600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr12:121439200-121451800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr12:121439400-121451600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:121439400-121451600	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr12:121439400-121451800	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:121439600-121451600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
20	chr12:121439600-121451600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:121439600-121451800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr12:121439600-121453600	Weak transcription	Stomach Mucosa	stomach
23	chr12:121439800-121451600	Strong transcription	Primary monocytes fromperipheralblood	blood
24	chr12:121440000-121451800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:121440400-121451800	Strong transcription	Primary B cells from peripheral blood	blood
26	chr12:121441000-121451600	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:121441000-121451800	Strong transcription	Dnd41	blood
28	chr12:121441400-121451600	Strong transcription	HepG2	liver
29	chr12:121442400-121453000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr12:121442800-121452600	Weak transcription	HMEC	breast
31	chr12:121442800-121453600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr12:121443600-121451600	Strong transcription	Fetal Intestine Small	intestine
33	chr12:121444800-121451600	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr12:121444800-121451600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:121445000-121451600	Strong transcription	H9 Cell Line	embryonic stem cell
36	chr12:121445000-121451600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:121445000-121451600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr12:121445200-121451600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr12:121445200-121451800	Strong transcription	NHLF	lung
40	chr12:121445400-121451600	Strong transcription	Duodenum Mucosa	Duodenum
41	chr12:121445400-121453000	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr12:121446400-121451800	Strong transcription	Colon Smooth Muscle	Colon
43	chr12:121448800-121453000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr12:121448800-121453000	Weak transcription	Fetal Kidney	kidney
45	chr12:121448800-121453000	Weak transcription	NHDF-Ad	bronchial
46	chr12:121448800-121453400	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr12:121448800-121453600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr12:121449000-121452600	Weak transcription	Hela-S3	cervix
49	chr12:121449000-121452800	Weak transcription	Brain Substantia Nigra	brain
50	chr12:121449000-121452800	Weak transcription	Psoas Muscle	Psoas

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