Variant report

Variant	rs12100650
Chromosome Location	chr14:72243873-72243874
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	chr14:72242483..72244393-chr14:72249540..72252223,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1954692	0.89[EUR][1000 genomes]
rs7146548	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7152273	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72730000	0.93[AFR][1000 genomes];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8017068	0.93[AFR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][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	esv3398985	chr14:71927884-72404676	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv530794	chr14:72113818-73034008	Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1047559	chr14:72151736-72282151	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12100650	PNMA1	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:72241400-72250400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr14:72242600-72244000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr14:72243000-72244800	Enhancers	Dnd41	blood
4	chr14:72243200-72244000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr14:72243200-72244200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr14:72243200-72244400	Enhancers	iPS-18 Cell Line	embryonic stem cell
7	chr14:72243200-72244600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr14:72243200-72244600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr14:72243200-72244800	Enhancers	H1 Cell Line	embryonic stem cell
10	chr14:72243200-72244800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr14:72243200-72244800	Enhancers	H9 Cell Line	embryonic stem cell
12	chr14:72243200-72244800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr14:72243200-72244800	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr14:72243200-72244800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr14:72243400-72244000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr14:72243400-72244200	Enhancers	HUVEC	blood vessel
17	chr14:72243400-72244200	Enhancers	NH-A	brain
18	chr14:72243400-72244600	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr14:72243600-72244000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr14:72243600-72244800	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr14:72243800-72244000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr14:72243800-72244000	Enhancers	GM12878-XiMat	blood
23	chr14:72243800-72244200	Enhancers	Lung	lung
24	chr14:72243800-72244800	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr14:72243800-72244800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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