Variant report

Variant	rs11059675
Chromosome Location	chr12:122668326-122668327
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	chr12:122667990-122668392	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: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10847516	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11058789	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11059472	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11059505	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11608363	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11611988	0.83[AMR][1000 genomes]
rs11613060	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12816786	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12828783	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4040811	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4372487	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs61954257	0.80[AMR][1000 genomes]
rs6489217	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305669	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7953139	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7955910	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7968808	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7972875	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7972979	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11059675	MLXIP	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122667200-122668400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr12:122667200-122668400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
3	chr12:122667200-122668400	Active TSS	Primary T cells from cord blood	blood
4	chr12:122667200-122668400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr12:122667200-122668400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr12:122667200-122668400	Active TSS	Brain Anterior Caudate	brain
7	chr12:122667200-122668400	Bivalent/Poised TSS	Monocytes-CD14+_RO01746	blood
8	chr12:122667400-122668400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr12:122667400-122668400	Active TSS	H9 Cell Line	embryonic stem cell
10	chr12:122667400-122668400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
11	chr12:122667400-122668400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
12	chr12:122667400-122668400	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr12:122667400-122668400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
14	chr12:122667400-122668400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:122667400-122668400	Active TSS	Brain Angular Gyrus	brain
16	chr12:122667400-122668400	Bivalent Enhancer	Stomach Mucosa	stomach
17	chr12:122667400-122669200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:122667600-122668400	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr12:122667600-122668400	Enhancers	Lung	lung
20	chr12:122667600-122668400	Bivalent/Poised TSS	Rectal Mucosa Donor 31	rectum
21	chr12:122667600-122668400	Active TSS	Osteobl	bone
22	chr12:122667600-122668600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
23	chr12:122667800-122668400	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr12:122667800-122670400	Enhancers	Spleen	Spleen
25	chr12:122668000-122668400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:122668000-122668400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:122668000-122668400	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr12:122668000-122668400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
29	chr12:122668000-122668400	Flanking Active TSS	Primary hematopoietic stem cells	blood
30	chr12:122668000-122668400	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
31	chr12:122668000-122668400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
32	chr12:122668000-122668400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr12:122668000-122668400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr12:122668000-122668400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:122668000-122668400	Flanking Active TSS	Adipose Nuclei	Adipose
36	chr12:122668000-122668400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr12:122668000-122668600	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr12:122668000-122669400	Enhancers	GM12878-XiMat	blood
39	chr12:122668200-122668400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr12:122668200-122668400	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
41	chr12:122668200-122668400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:122668200-122668400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
43	chr12:122668200-122668400	Flanking Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr12:122668200-122668400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
45	chr12:122668200-122668400	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
46	chr12:122668200-122668400	Enhancers	Muscle Satellite Cultured Cells	--
47	chr12:122668200-122668400	Enhancers	Cortex derived primary cultured neurospheres	brain
48	chr12:122668200-122668400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr12:122668200-122668400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:122668200-122668400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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