Variant report

Variant	rs12899647
Chromosome Location	chr15:55974954-55974955
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	chr15:55973838..55975695-chr15:56033955..56035878,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000166450	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1011061	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10152116	1.00[ASN][1000 genomes]
rs10152830	1.00[ASN][1000 genomes]
rs10851590	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071203	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632579	0.82[ASN][1000 genomes]
rs11639086	1.00[ASN][1000 genomes]
rs11852746	1.00[ASN][1000 genomes]
rs11853533	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11855737	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11857254	1.00[ASN][1000 genomes]
rs11857271	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12438394	1.00[ASN][1000 genomes]
rs12439011	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12440103	1.00[ASN][1000 genomes]
rs12442165	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12899976	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12901963	1.00[ASN][1000 genomes]
rs12903239	1.00[ASN][1000 genomes]
rs12905693	1.00[ASN][1000 genomes]
rs12906885	1.00[ASN][1000 genomes]
rs12907557	1.00[ASN][1000 genomes]
rs12907772	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907892	1.00[ASN][1000 genomes]
rs12908232	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12908813	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12910180	1.00[ASN][1000 genomes]
rs12911682	1.00[ASN][1000 genomes]
rs12912118	0.90[ASN][1000 genomes]
rs12914863	1.00[ASN][1000 genomes]
rs12915092	0.90[ASN][1000 genomes]
rs12915423	0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34303822	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3985768	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4412917	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4774222	1.00[ASN][1000 genomes]
rs55874929	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66519039	1.00[ASN][1000 genomes]
rs8028880	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	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
9	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12899647	PRTG	cis	Thyroid	GTEx

Chromatin state (count:38 , 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	chr15:55954000-55975400	Weak transcription	HSMM	muscle
5	chr15:55954000-55977400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:55954400-55987000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:55954600-55975000	Weak transcription	A549	lung
8	chr15:55955400-55980000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr15:55958200-55977600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr15:55958800-55977400	Weak transcription	Left Ventricle	heart
11	chr15:55960400-55977600	Weak transcription	Placenta	Placenta
12	chr15:55960800-55995800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:55963400-55980200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:55964000-55977200	Weak transcription	HUVEC	blood vessel
15	chr15:55964200-55975600	Weak transcription	Fetal Stomach	stomach
16	chr15:55964800-55977200	Weak transcription	HepG2	liver
17	chr15:55969000-55975600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:55969000-55976000	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:55969000-55976800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:55969000-55987000	Weak transcription	Fetal Lung	lung
21	chr15:55969200-55975600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr15:55969200-55980200	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr15:55969200-55986000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:55969400-55980200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr15:55970400-55977800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr15:55970600-55976800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:55970800-55977400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:55971200-55976200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:55972000-55986400	Weak transcription	Fetal Intestine Large	intestine
30	chr15:55973600-55975400	Weak transcription	Right Atrium	heart
31	chr15:55973800-55976000	Strong transcription	Fetal Kidney	kidney
32	chr15:55974200-55976000	Strong transcription	Hela-S3	cervix
33	chr15:55974200-55976800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:55974200-55978600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:55974400-55976000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:55974400-55976200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:55974600-55976000	Weak transcription	GM12878-XiMat	blood
38	chr15:55974600-55977800	Weak transcription	Primary hematopoietic stem cells	blood

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