Variant report

Variant	rs2069389
Chromosome Location	chr12:56359642-56359643
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	chr12:56359594-56361350	ECC-1	luminal epithelium:	n/a	n/a
2	SP1	chr12:56359618-56361191	H1-hESC	embryonic stem cell:	n/a	chr12:56360535-56360547 chr12:56360564-56360576 chr12:56360566-56360575 chr12:56360565-56360575 chr12:56360537-56360546 chr12:56360536-56360545 chr12:56360564-56360576 chr12:56360565-56360575 chr12:56360566-56360575 chr12:56360517-56360538 chr12:56360535-56360547 chr12:56360532-56360546 chr12:56360565-56360574
3	SIN3A	chr12:56359099-56361358	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr12:56359580-56359902	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr12:56359332-56361169	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr12:56359595-56360823	H1-hESC	embryonic stem cell:	n/a	n/a
7	ZBTB7A	chr12:56359563-56361328	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:56351426..56355339-chr12:56358310..56361732,4	K562	blood:
2	chr12:56348195..56352007-chr12:56357444..56361194,9	MCF-7	breast:
3	chr12:56222205..56224922-chr12:56358822..56360561,2	MCF-7	breast:
4	chr12:56132724..56138260-chr12:56359199..56362083,4	MCF-7	breast:
5	chr12:56319178..56327497-chr12:56356755..56363470,19	MCF-7	breast:
6	chr12:56319082..56322613-chr12:56358459..56362927,5	MCF-7	breast:
7	chr12:56359297..56361313-chr17:56079815..56082507,2	MCF-7	breast:
8	chr12:56135390..56138217-chr12:56359317..56362756,4	K562	blood:
9	chr12:56137714..56140365-chr12:56357823..56359746,2	K562	blood:
10	chr12:56325013..56327160-chr12:56358376..56361876,4	MCF-7	breast:
11	chr12:56208204..56214844-chr12:56359426..56363484,9	MCF-7	breast:
12	chr12:56334256..56336718-chr12:56359485..56361088,3	K562	blood:
13	chr12:56332251..56334580-chr12:56358536..56360583,2	MCF-7	breast:
14	chr12:56319307..56323047-chr12:56359033..56361996,7	K562	blood:
15	chr12:56357871..56361008-chr12:56510432..56513466,3	K562	blood:
16	chr12:56318129..56322590-chr12:56359033..56362321,5	K562	blood:

Variant related genes	Relation type
CDK2	TF binding region
ENSG00000135482	Chromatin interaction
ENSG00000136450	Chromatin interaction
ENSG00000182796	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000065357	Chromatin interaction
ENSG00000139641	Chromatin interaction
ENSG00000135392	Chromatin interaction
ENSG00000205323	Chromatin interaction
ENSG00000170473	Chromatin interaction
ENSG00000185664	Chromatin interaction
ENSG00000229117	Chromatin interaction
ENSG00000123353	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:1)

rs_ID	r²[population]
rs57343616	1.00[AFR][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	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
3	nsv1043988	chr12:56348185-56534900	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	189 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2069389	TMEM4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56346600-56360000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:56347200-56360000	Weak transcription	HSMMtube	muscle
3	chr12:56347400-56359800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr12:56347400-56359800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr12:56347600-56359800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:56348200-56360000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:56348400-56359800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:56348400-56359800	Weak transcription	Fetal Lung	lung
9	chr12:56350000-56359800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:56351600-56359800	Weak transcription	Primary T cells from cord blood	blood
11	chr12:56351800-56359800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:56351800-56359800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr12:56351800-56359800	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr12:56352000-56359800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr12:56354000-56359800	Weak transcription	K562	blood
16	chr12:56355400-56359800	Weak transcription	Lung	lung
17	chr12:56358000-56363200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr12:56358600-56361200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr12:56358800-56361800	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr12:56359000-56360200	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
21	chr12:56359000-56361400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr12:56359000-56361400	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr12:56359000-56361600	Active TSS	H9 Cell Line	embryonic stem cell
24	chr12:56359200-56359800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:56359200-56359800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr12:56359200-56359800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr12:56359200-56359800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr12:56359200-56359800	Enhancers	Colonic Mucosa	Colon
29	chr12:56359200-56360000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:56359200-56360200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
31	chr12:56359200-56360400	Flanking Active TSS	H1 Cell Line	embryonic stem cell
32	chr12:56359200-56360400	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr12:56359200-56360400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr12:56359200-56361400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:56359200-56361600	Active TSS	ES-I3 Cell Line	embryonic stem cell
36	chr12:56359400-56359800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
37	chr12:56359400-56359800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:56359400-56359800	Enhancers	Liver	Liver
39	chr12:56359400-56359800	Enhancers	Fetal Intestine Small	intestine
40	chr12:56359400-56360000	Enhancers	Primary B cells from peripheral blood	blood
41	chr12:56359400-56360000	Enhancers	Adipose Nuclei	Adipose
42	chr12:56359400-56360000	Enhancers	Brain Anterior Caudate	brain
43	chr12:56359400-56360000	Enhancers	Fetal Kidney	kidney
44	chr12:56359400-56360000	Enhancers	Placenta	Placenta
45	chr12:56359400-56360000	Enhancers	Fetal Stomach	stomach
46	chr12:56359400-56360000	Enhancers	Ovary	ovary
47	chr12:56359400-56360000	Enhancers	Placenta Amnion	Placenta Amnion
48	chr12:56359400-56360000	Enhancers	Dnd41	blood
49	chr12:56359400-56360200	Enhancers	Fetal Heart	heart
50	chr12:56359400-56361400	Active TSS	ES-WA7 Cell Line	embryonic stem cell

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