Variant report

Variant	rs4774220
Chromosome Location	chr15:55962861-55962862
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	chr15:55961153..55963651-chr15:56033694..56036455,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166450	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10518817	0.90[ASN][1000 genomes]
rs10851589	0.88[ASN][1000 genomes]
rs11852298	0.90[ASN][1000 genomes]
rs11854213	0.89[ASN][1000 genomes]
rs12373006	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12438177	0.96[ASN][1000 genomes]
rs12903822	0.96[ASN][1000 genomes]
rs1438918	0.89[ASN][1000 genomes]
rs16976450	0.90[ASN][1000 genomes]
rs16976472	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1986012	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2118781	0.88[ASN][1000 genomes]
rs2414424	0.82[ASN][1000 genomes]
rs2414426	0.81[ASN][1000 genomes]
rs28556884	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28557162	0.80[AFR][1000 genomes]
rs4392003	0.94[ASN][1000 genomes]
rs4774799	0.80[ASN][1000 genomes]
rs4774800	0.88[ASN][1000 genomes]
rs62043869	0.88[ASN][1000 genomes]
rs6493805	0.89[ASN][1000 genomes]
rs7162504	0.80[AFR][1000 genomes]
rs7162879	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7165778	0.86[ASN][1000 genomes]
rs7166952	0.89[ASN][1000 genomes]
rs7171318	0.89[ASN][1000 genomes]
rs7171522	0.88[ASN][1000 genomes]
rs7171834	0.88[ASN][1000 genomes]
rs7178379	0.88[ASN][1000 genomes]
rs8025445	0.81[ASN][1000 genomes]
rs8034113	0.90[ASN][1000 genomes]
rs9920076	0.86[ASN][1000 genomes]
rs9920246	0.86[ASN][1000 genomes]
rs9920262	0.88[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4774220	PRTG	cis	Thyroid	GTEx

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55911800-55977000	Weak transcription	Fetal Intestine Small	intestine
2	chr15:55920800-55987600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:55932600-55987000	Weak transcription	Ovary	ovary
4	chr15:55932800-55973400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr15:55942800-55974400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr15:55952800-55972000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:55953800-55964800	Weak transcription	Right Ventricle	heart
8	chr15:55954000-55968600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:55954000-55971600	Weak transcription	Fetal Kidney	kidney
10	chr15:55954000-55975400	Weak transcription	HSMM	muscle
11	chr15:55954000-55977400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:55954200-55964400	Weak transcription	Fetal Lung	lung
13	chr15:55954200-55970000	Weak transcription	Fetal Intestine Large	intestine
14	chr15:55954400-55964400	Weak transcription	HepG2	liver
15	chr15:55954400-55987000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:55954600-55975000	Weak transcription	A549	lung
17	chr15:55955200-55968400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr15:55955400-55963800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr15:55955400-55980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:55955600-55963000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr15:55957000-55965600	Weak transcription	Lung	lung
22	chr15:55958200-55977600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:55958800-55977400	Weak transcription	Left Ventricle	heart
24	chr15:55959000-55963200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:55959000-55973800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr15:55960000-55963800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:55960400-55977600	Weak transcription	Placenta	Placenta
28	chr15:55960800-55995800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr15:55961000-55963800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:55961400-55963400	Weak transcription	Fetal Stomach	stomach
31	chr15:55961400-55972400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:55961400-55973000	Weak transcription	Psoas Muscle	Psoas
33	chr15:55961600-55966000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:55962000-55963400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:55962000-55963600	Weak transcription	Gastric	stomach
36	chr15:55962000-55968000	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr15:55962000-55968000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:55962600-55964800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr15:55962600-55974800	Weak transcription	Fetal Muscle Leg	muscle

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