Variant report

Variant	rs4774800
Chromosome Location	chr15:55950941-55950942
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55948774..55951298-chr15:56033579..56035270,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166450	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10518817	0.91[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs10851589	0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs11852298	0.83[ASN][1000 genomes]
rs11854213	0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs12373006	0.86[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs12438177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12591246	0.81[CHB][hapmap]
rs12592192	0.80[ASN][1000 genomes]
rs12903822	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs1438918	0.83[ASN][1000 genomes]
rs16976450	0.95[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.94[ASN][1000 genomes]
rs16976472	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs2118781	0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[ASN][1000 genomes]
rs2414424	0.86[CHB][hapmap]
rs2414426	0.86[CHB][hapmap]
rs2414427	0.86[CHB][hapmap]
rs28556884	0.87[ASN][1000 genomes]
rs4392003	0.86[ASN][1000 genomes]
rs4774220	0.88[ASN][1000 genomes]
rs4774799	0.92[ASN][1000 genomes]
rs572531	0.88[CHD][hapmap];0.85[GIH][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs62043869	0.94[ASN][1000 genomes]
rs62043871	0.88[ASN][1000 genomes]
rs6493805	0.93[ASN][1000 genomes]
rs7162879	0.86[CHB][hapmap];0.82[ASN][1000 genomes]
rs7165778	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7166952	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7171318	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7171522	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7171834	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7178379	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7180112	0.81[ASN][1000 genomes]
rs8025445	0.82[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs8034113	0.96[ASN][1000 genomes]
rs9920076	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9920246	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9920262	0.82[AFR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv457158	chr15:55930542-55982257	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv569541	chr15:55930542-55982257	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4774800	AP4E1	cis	parietal	SCAN
rs4774800	MYO5C	cis	parietal	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55911800-55977000	Weak transcription	Fetal Intestine Small	intestine
2	chr15:55920600-55953400	Weak transcription	HUVEC	blood vessel
3	chr15:55920800-55987600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:55932600-55987000	Weak transcription	Ovary	ovary
5	chr15:55932800-55973400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:55933400-55953200	Weak transcription	HepG2	liver
7	chr15:55933400-55953400	Weak transcription	Fetal Intestine Large	intestine
8	chr15:55939200-55953400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:55942800-55974400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr15:55945000-55951800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr15:55945000-55953200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:55945200-55951200	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr15:55945200-55952400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:55945400-55952400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr15:55945600-55951200	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr15:55945600-55951200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr15:55946000-55953400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:55946200-55951400	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:55947200-55951200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr15:55947400-55951200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:55947400-55952400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr15:55947400-55960200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr15:55948200-55952400	Weak transcription	Fetal Kidney	kidney
24	chr15:55948200-55953600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:55948600-55951200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:55949800-55952400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:55950800-55952000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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