Variant report

Variant	rs2009345
Chromosome Location	chr6:150389748-150389749
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:150378184..150381057-chr6:150388223..150390154,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs2010259	0.81[JPT][hapmap]
rs2065713	0.92[CEU][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2343271	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs470138	0.81[JPT][hapmap]
rs4869816	0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs550193	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6920314	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6941524	1.00[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs912556	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs932744	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9371692	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9371693	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[LWK][hapmap];0.90[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9397137	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs9397622	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv3323918	chr6:150327978-150392099	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv886767	chr6:150335407-150400488	Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1026236	chr6:150360882-150408946	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2009345	PPP1R14C	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150388600-150390000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr6:150389200-150389800	Enhancers	Spleen	Spleen
3	chr6:150389200-150389800	Flanking Active TSS	NHLF	lung
4	chr6:150389200-150389800	Flanking Active TSS	Osteobl	bone
5	chr6:150389200-150390000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:150389200-150390200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr6:150389200-150390600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr6:150389200-150390800	Flanking Active TSS	Stomach Smooth Muscle	stomach
9	chr6:150389200-150391000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
10	chr6:150389400-150389800	Flanking Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:150389400-150389800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:150389400-150389800	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:150389400-150389800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
14	chr6:150389400-150389800	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr6:150389400-150389800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr6:150389400-150389800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
17	chr6:150389400-150389800	Enhancers	Fetal Brain Male	brain
18	chr6:150389400-150389800	Flanking Active TSS	Fetal Kidney	kidney
19	chr6:150389400-150389800	Flanking Active TSS	NH-A	brain
20	chr6:150389400-150390000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr6:150389400-150390000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
22	chr6:150389400-150390000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
23	chr6:150389400-150390000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr6:150389400-150390000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr6:150389400-150390000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
26	chr6:150389400-150390000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:150389400-150390000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr6:150389400-150390000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:150389400-150390000	Flanking Active TSS	Duodenum Mucosa	Duodenum
30	chr6:150389400-150390000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
31	chr6:150389400-150390000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
32	chr6:150389400-150390000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
33	chr6:150389400-150390000	Flanking Active TSS	HMEC	breast
34	chr6:150389400-150390000	Flanking Active TSS	HUVEC	blood vessel
35	chr6:150389400-150390800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
36	chr6:150389400-150390800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
37	chr6:150389400-150390800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr6:150389400-150390800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr6:150389400-150390800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr6:150389400-150390800	Flanking Active TSS	Adipose Nuclei	Adipose
41	chr6:150389400-150390800	Active TSS	Brain Cingulate Gyrus	brain
42	chr6:150389400-150390800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
43	chr6:150389400-150390800	Active TSS	HSMMtube	muscle
44	chr6:150389400-150390800	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
45	chr6:150389400-150390800	Active TSS	NHDF-Ad	bronchial
46	chr6:150389400-150391000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
47	chr6:150389400-150391000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr6:150389400-150391000	Active TSS	Brain Anterior Caudate	brain
49	chr6:150389400-150391000	Active TSS	Pancreatic Islets	Pancreatic Islet
50	chr6:150389400-150391000	Active TSS	Rectal Smooth Muscle	rectum

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