Variant report

Variant	rs1798588
Chromosome Location	chr12:32312547-32312548
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:32311735..32314628-chr17:57918387..57920948,2	MCF-7	breast:
2	chr12:32293794..32295739-chr12:32312256..32314518,2	K562	blood:

Variant related genes	Relation type
ENSG00000199004	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10844145	0.84[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs10844146	0.93[ASN][1000 genomes]
rs11051827	0.93[ASN][1000 genomes]
rs1151015	0.87[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs61926906	0.91[ASN][1000 genomes]
rs7967654	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3363806	chr12:31872264-32410283	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	esv3508621	chr12:31872654-32410593	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	esv3508622	chr12:31872654-32410593	Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv983498	chr12:32153446-32388092	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv898969	chr12:32224948-32375677	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1042317	chr12:32228872-32316774	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1041733	chr12:32247427-32312547	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv531960	chr12:32257285-32775277	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	esv2751096	chr12:32280340-32702784	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
10	nsv558171	chr12:32287259-32559693	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1798588	FAM60A	cis	parietal	SCAN
rs1798588	TMTC1	cis	cerebellum	SCAN
rs1798588	DENND5B	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:32269000-32340200	Weak transcription	Dnd41	blood
2	chr12:32287800-32328400	Weak transcription	Aorta	Aorta
3	chr12:32293000-32316000	Weak transcription	HUVEC	blood vessel
4	chr12:32293600-32323600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:32293600-32369200	Weak transcription	Thymus	Thymus
6	chr12:32294200-32318200	Weak transcription	Primary T cells from cord blood	blood
7	chr12:32296200-32313800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr12:32298400-32312800	Weak transcription	Brain Angular Gyrus	brain
9	chr12:32299400-32312600	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr12:32299400-32334800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr12:32299600-32346200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:32300200-32319200	Weak transcription	GM12878-XiMat	blood
13	chr12:32300200-32336600	Weak transcription	A549	lung
14	chr12:32300400-32312600	Weak transcription	Stomach Smooth Muscle	stomach
15	chr12:32301600-32316200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr12:32301800-32312800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:32303000-32317800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr12:32303000-32319200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr12:32303000-32336600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr12:32303400-32314600	Weak transcription	Primary B cells from cord blood	blood
21	chr12:32303800-32319400	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:32304800-32317800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr12:32307600-32312600	Weak transcription	Spleen	Spleen
24	chr12:32308000-32312600	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr12:32309000-32312600	Weak transcription	Brain Germinal Matrix	brain
26	chr12:32309400-32312800	Weak transcription	Brain Hippocampus Middle	brain
27	chr12:32309400-32312800	Weak transcription	Brain Substantia Nigra	brain
28	chr12:32309400-32312800	Weak transcription	Fetal Heart	heart
29	chr12:32309400-32313600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr12:32309400-32315000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr12:32309400-32323200	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:32309400-32324000	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr12:32309400-32325000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:32309400-32353400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:32309600-32317200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:32309600-32323000	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr12:32309600-32323000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:32309600-32336400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:32309600-32346000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:32309600-32351400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:32309600-32352200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr12:32309800-32323000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr12:32309800-32336400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr12:32309800-32336600	Weak transcription	HMEC	breast
45	chr12:32310200-32313600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr12:32310800-32322800	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr12:32310800-32323000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr12:32310800-32323400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr12:32311400-32313400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:32311400-32313600	Enhancers	Cortex derived primary cultured neurospheres	brain

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