Variant report

Variant	rs2292443
Chromosome Location	chr12:122668091-122668092
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	ELF1	chr12:122667478-122668120	GM12878	blood:	n/a	n/a
2	USF1	chr12:122667958-122668177	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr12:122667990-122668392	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122458978..122460744-chr12:122667663..122669885,2	MCF-7	breast:

Variant related genes	Relation type
LRRC43	TF binding region
ENSG00000110987	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10744239	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10773171	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10846939	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10846976	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10846977	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10847623	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11058323	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12371561	0.83[JPT][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12424694	0.88[CEU][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12427088	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2175531	0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35242277	0.82[AMR][1000 genomes]
rs35822906	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4447210	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4758679	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4758680	1.00[CEU][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4758681	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4758682	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4758683	0.83[EUR][1000 genomes]
rs61955561	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6488994	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6489188	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7303129	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7311842	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7311871	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7964127	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7979259	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases
2	nsv916686	chr12:122240149-122714056	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
3	nsv527450	chr12:122481290-122676531	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1038827	chr12:122627371-122687913	Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2292443	UCHL1	trans	lymphoblastoid	seeQTL
rs2292443	RHOF	cis	parietal	SCAN
rs2292443	GPR81	cis	cerebellum	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122667200-122668200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
2	chr12:122667200-122668200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr12:122667200-122668200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:122667200-122668200	Active TSS	A549	lung
5	chr12:122667200-122668400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
6	chr12:122667200-122668400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
7	chr12:122667200-122668400	Active TSS	Primary T cells from cord blood	blood
8	chr12:122667200-122668400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr12:122667200-122668400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr12:122667200-122668400	Active TSS	Brain Anterior Caudate	brain
11	chr12:122667200-122668400	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
12	chr12:122667400-122668200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
13	chr12:122667400-122668200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr12:122667400-122668200	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr12:122667400-122668200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr12:122667400-122668200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr12:122667400-122668200	Flanking Active TSS	Primary B cells from cord blood	blood
18	chr12:122667400-122668200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
19	chr12:122667400-122668200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
20	chr12:122667400-122668200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
21	chr12:122667400-122668200	Active TSS	Brain Inferior Temporal Lobe	brain
22	chr12:122667400-122668200	Active TSS	Colon Smooth Muscle	Colon
23	chr12:122667400-122668200	Active TSS	Duodenum Mucosa	Duodenum
24	chr12:122667400-122668200	Bivalent/Poised TSS	Fetal Brain Female	brain
25	chr12:122667400-122668200	Active TSS	Fetal Kidney	kidney
26	chr12:122667400-122668200	Active TSS	Ovary	ovary
27	chr12:122667400-122668200	Bivalent/Poised TSS	Placenta Amnion	Placenta Amnion
28	chr12:122667400-122668200	Bivalent/Poised TSS	HepG2	liver
29	chr12:122667400-122668400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
30	chr12:122667400-122668400	Active TSS	H9 Cell Line	embryonic stem cell
31	chr12:122667400-122668400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
32	chr12:122667400-122668400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr12:122667400-122668400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:122667400-122668400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr12:122667400-122668400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr12:122667400-122668400	Active TSS	Brain Angular Gyrus	brain
37	chr12:122667400-122668400	Bivalent Enhancer	Stomach Mucosa	stomach
38	chr12:122667400-122669200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:122667600-122668200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
40	chr12:122667600-122668200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr12:122667600-122668200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:122667600-122668200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:122667600-122668200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:122667600-122668200	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
45	chr12:122667600-122668200	Bivalent Enhancer	Fetal Brain Male	brain
46	chr12:122667600-122668200	Active TSS	Fetal Intestine Large	intestine
47	chr12:122667600-122668200	Active TSS	HUVEC	blood vessel
48	chr12:122667600-122668200	Active TSS	NH-A	brain
49	chr12:122667600-122668400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr12:122667600-122668400	Enhancers	Lung	lung

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