Variant report

Variant	rs12942391
Chromosome Location	chr17:37733737-37733738
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:37728576..37732593-chr17:37732827..37737352,4	MCF-7	breast:

Extended variants
information (count: 84 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1054488	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10775391	0.83[ASN][1000 genomes]
rs1077715	0.83[ASN][1000 genomes]
rs10852933	0.85[ASN][1000 genomes]
rs11078910	0.81[ASN][1000 genomes]
rs11078911	0.81[ASN][1000 genomes]
rs11078912	0.81[ASN][1000 genomes]
rs11078913	0.81[ASN][1000 genomes]
rs11078915	0.86[ASN][1000 genomes]
rs11654018	0.86[ASN][1000 genomes]
rs11655531	0.85[ASN][1000 genomes]
rs11657058	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11657153	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11658219	0.86[ASN][1000 genomes]
rs11658678	0.83[ASN][1000 genomes]
rs12150047	0.83[ASN][1000 genomes]
rs12449852	0.81[ASN][1000 genomes]
rs12450559	0.83[ASN][1000 genomes]
rs12936996	0.81[ASN][1000 genomes]
rs12937013	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12938099	0.83[ASN][1000 genomes]
rs12941619	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12947506	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12952384	0.81[ASN][1000 genomes]
rs1619021	0.83[ASN][1000 genomes]
rs1874226	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1877030	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2303316	0.86[ASN][1000 genomes]
rs35335692	0.86[ASN][1000 genomes]
rs364989	0.83[ASN][1000 genomes]
rs3889368	0.83[ASN][1000 genomes]
rs412430	0.83[ASN][1000 genomes]
rs4239222	0.85[ASN][1000 genomes]
rs4332770	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4357971	0.86[ASN][1000 genomes]
rs439537	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4488484	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4591174	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4794813	0.81[ASN][1000 genomes]
rs4794814	0.85[ASN][1000 genomes]
rs4795367	0.83[ASN][1000 genomes]
rs4795375	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4795376	0.81[ASN][1000 genomes]
rs4795377	0.81[ASN][1000 genomes]
rs4795379	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4795381	0.85[ASN][1000 genomes]
rs4795382	0.84[ASN][1000 genomes]
rs4795384	0.86[ASN][1000 genomes]
rs4795385	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55660616	0.83[ASN][1000 genomes]
rs6503519	0.86[ASN][1000 genomes]
rs6503520	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6503521	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7216086	0.86[ASN][1000 genomes]
rs7406928	0.83[ASN][1000 genomes]
rs7503069	0.85[ASN][1000 genomes]
rs7503377	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7503514	0.81[ASN][1000 genomes]
rs7503705	0.81[ASN][1000 genomes]
rs8065963	0.83[ASN][1000 genomes]
rs8067511	0.82[ASN][1000 genomes]
rs8067884	0.81[ASN][1000 genomes]
rs8069074	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8073248	0.87[ASN][1000 genomes]
rs8074276	0.84[ASN][1000 genomes]
rs8074855	0.83[ASN][1000 genomes]
rs8075737	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8081528	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8182252	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs903507	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9646419	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932024	chr17:37192290-37850932	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	92 gene(s)	inside rSNPs	diseases
2	nsv1066033	chr17:37333956-37795617	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	78 gene(s)	inside rSNPs	diseases
3	nsv543340	chr17:37333956-37795617	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers 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	78 gene(s)	inside rSNPs	diseases
4	nsv1061951	chr17:37442228-37770903	Bivalent Enhancer Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
5	nsv543341	chr17:37442228-37770903	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
6	esv1825702	chr17:37487168-37876767	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
7	nsv532712	chr17:37521822-37768345	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
8	nsv833442	chr17:37692880-37861291	Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
9	nsv521294	chr17:37694709-37804858	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
10	nsv908205	chr17:37709422-37830900	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	nsv908206	chr17:37709422-37866005	Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
12	nsv908207	chr17:37709422-37922259	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
13	nsv833443	chr17:37725640-37882864	Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12942391	PGAP3	cis	Thyroid	GTEx
rs12942391	CRKRS	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:37721400-37736200	Weak transcription	Fetal Heart	heart
2	chr17:37730400-37735400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr17:37730600-37734200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr17:37730600-37734200	Weak transcription	Liver	Liver
5	chr17:37730600-37734200	Weak transcription	Fetal Lung	lung
6	chr17:37730600-37734400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:37730600-37734600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr17:37730600-37734800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr17:37730600-37734800	Weak transcription	Lung	lung
10	chr17:37730600-37734800	Weak transcription	Pancreas	Pancrea
11	chr17:37730600-37741400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr17:37730600-37741600	Weak transcription	Right Atrium	heart
13	chr17:37730600-37748000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr17:37730800-37734800	Weak transcription	Left Ventricle	heart
15	chr17:37730800-37738600	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr17:37731400-37734600	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr17:37733000-37734200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr17:37733000-37734800	Weak transcription	Brain Germinal Matrix	brain
19	chr17:37733000-37735000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr17:37733400-37734200	Weak transcription	Fetal Brain Female	brain
21	chr17:37733400-37734600	Weak transcription	Fetal Brain Male	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links