Variant report

Variant	rs12442771
Chromosome Location	chr15:56032099-56032100
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	chr15:56013890..56016353-chr15:56030511..56032311,2	MCF-7	breast:
2	chr15:56031905..56035384-chr15:56036677..56038977,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259369	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10518817	0.81[CHB][hapmap]
rs10851589	0.81[CHB][hapmap]
rs10851591	0.87[ASN][1000 genomes]
rs11630141	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11854213	0.81[CHB][hapmap]
rs11858195	0.84[MEX][hapmap]
rs12373006	0.85[CHB][hapmap]
rs12591246	0.91[CHB][hapmap]
rs16976472	0.81[CHB][hapmap]
rs1814329	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2008336	0.95[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2118781	0.85[CHB][hapmap]
rs2414424	0.86[CHB][hapmap]
rs2414426	0.86[CHB][hapmap]
rs2414427	0.86[CHB][hapmap]
rs2414430	0.85[ASN][1000 genomes]
rs2414431	0.95[CHB][hapmap];0.85[CHD][hapmap];0.87[ASN][1000 genomes]
rs28485308	0.81[ASN][1000 genomes]
rs28575567	0.80[ASN][1000 genomes]
rs4377101	0.95[CHB][hapmap];0.85[CHD][hapmap]
rs4774802	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4774803	0.87[ASN][1000 genomes]
rs57782071	0.92[ASN][1000 genomes]
rs62043907	0.84[ASN][1000 genomes]
rs62043908	0.88[ASN][1000 genomes]
rs6493809	0.90[CHB][hapmap];0.85[CHD][hapmap];0.80[ASN][1000 genomes]
rs6493814	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs687128	0.96[CEU][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs7161967	0.80[ASN][1000 genomes]
rs7162371	0.87[ASN][1000 genomes]
rs7162879	0.85[CHB][hapmap]
rs7163167	0.85[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs7171318	0.81[CHB][hapmap]
rs7178379	0.81[CHB][hapmap]
rs7181212	0.95[CHB][hapmap]
rs7182733	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7359255	0.91[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8023911	0.80[ASN][1000 genomes]
rs8025445	0.81[CHB][hapmap]
rs8030795	0.89[ASN][1000 genomes]
rs8034414	0.88[ASN][1000 genomes]
rs8037136	0.95[CHB][hapmap];0.80[ASN][1000 genomes]
rs8038074	0.88[ASN][1000 genomes]
rs8042029	0.80[ASN][1000 genomes]
rs9920546	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv457157	chr15:55722213-56255774	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv569539	chr15:55722213-56255774	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	nsv1049774	chr15:55759573-56044600	Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
7	nsv833017	chr15:55965957-56157912	Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	esv3366380	chr15:56003224-56141650	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised 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	7 gene(s)	inside rSNPs	diseases
9	nsv1052495	chr15:56013617-56102164	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12442771	CCPG1	cis	parietal	SCAN
rs12442771	AP4E1	cis	parietal	SCAN
rs12442771	MYO5C	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56017800-56033400	Weak transcription	Ovary	ovary
2	chr15:56025000-56033600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:56027800-56033000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr15:56028800-56033600	Weak transcription	HSMM	muscle
5	chr15:56029800-56032200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr15:56029800-56033200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr15:56030000-56032600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr15:56030000-56032600	Weak transcription	Stomach Smooth Muscle	stomach
9	chr15:56030000-56032600	Weak transcription	A549	lung
10	chr15:56030000-56033400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr15:56030000-56033600	Weak transcription	Placenta	Placenta
12	chr15:56030200-56032600	Weak transcription	Fetal Intestine Large	intestine
13	chr15:56030200-56032800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:56030200-56032800	Weak transcription	Fetal Lung	lung
15	chr15:56030400-56034600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:56030600-56033400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr15:56030600-56034600	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:56031000-56032600	Weak transcription	Hela-S3	cervix
19	chr15:56031200-56032200	Enhancers	Placenta Amnion	Placenta Amnion
20	chr15:56031200-56033000	Weak transcription	Fetal Stomach	stomach
21	chr15:56031200-56033600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr15:56031200-56033600	Weak transcription	Psoas Muscle	Psoas
23	chr15:56031200-56034200	Transcr. at gene 5' and 3'	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:56031400-56036600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:56031600-56032200	Enhancers	Fetal Kidney	kidney
26	chr15:56031600-56033400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr15:56031600-56033800	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
28	chr15:56031800-56032200	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr15:56031800-56032200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
30	chr15:56031800-56033000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:56031800-56033200	Weak transcription	HUVEC	blood vessel
32	chr15:56032000-56032200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
33	chr15:56032000-56032200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
34	chr15:56032000-56032400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr15:56032000-56032600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:56032000-56033400	Enhancers	HepG2	liver

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