Variant report

Variant	rs13165504
Chromosome Location	chr5:42983387-42983388
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:42982424..42987523-chr5:43005404..43009945,6	MCF-7	breast:
2	chr5:42982268..42984810-chr5:43065924..43068317,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000172262	Chromatin interaction
ENSG00000271788	Chromatin interaction
ENSG00000177738	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1032434	0.82[ASN][1000 genomes]
rs10454865	0.85[ASN][1000 genomes]
rs10941608	0.81[ASN][1000 genomes]
rs11550285	0.88[ASN][1000 genomes]
rs11550286	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11550287	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11740797	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11742691	0.85[ASN][1000 genomes]
rs11743246	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11747015	0.89[ASN][1000 genomes]
rs11748187	0.82[ASN][1000 genomes]
rs11750239	0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11949817	0.82[ASN][1000 genomes]
rs11954543	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11956243	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12188691	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13155513	0.82[ASN][1000 genomes]
rs13159703	0.80[ASN][1000 genomes]
rs13169563	0.80[ASN][1000 genomes]
rs13173064	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13356944	0.92[ASN][1000 genomes]
rs17301375	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2452831	0.82[ASN][1000 genomes]
rs316405	0.82[ASN][1000 genomes]
rs316409	0.82[ASN][1000 genomes]
rs316410	0.82[ASN][1000 genomes]
rs316418	0.82[ASN][1000 genomes]
rs3207358	0.82[ASN][1000 genomes]
rs34087147	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34492794	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34808919	0.82[ASN][1000 genomes]
rs35085573	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35541316	0.82[ASN][1000 genomes]
rs36039989	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3733839	0.82[ASN][1000 genomes]
rs3797312	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3849698	0.89[ASN][1000 genomes]
rs3849699	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs493097	0.82[ASN][1000 genomes]
rs55939188	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56169202	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs581914	0.85[ASN][1000 genomes]
rs62367685	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62367688	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62372869	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs670206	0.80[ASN][1000 genomes]
rs6859096	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6864223	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6898323	0.83[AFR][1000 genomes]
rs7709181	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7727892	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7729529	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9790935	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
7	esv1813779	chr5:42906572-42992040	Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
8	nsv1029288	chr5:42928085-43047323	Flanking Bivalent TSS/Enh Active TSS Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	120 gene(s)	inside rSNPs	diseases
9	nsv1020910	chr5:42929799-43000021	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
10	nsv537738	chr5:42929799-43000021	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
11	nsv968169	chr5:42956713-43043472	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	116 gene(s)	inside rSNPs	diseases
12	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh 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 miRNA target site	283 gene(s)	inside rSNPs	diseases
13	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
14	nsv881436	chr5:42967215-43008917	Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
15	nsv880447	chr5:42967215-43030798	Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
16	nsv881640	chr5:42978644-43028221	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases
17	nsv880415	chr5:42978644-43030798	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	94 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13165504	ZNF131	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42962200-42984400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
2	chr5:42967000-42985600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr5:42969400-42985400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr5:42970800-42988400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr5:42971000-42984400	Weak transcription	Primary B cells from cord blood	blood
6	chr5:42971000-42985400	Weak transcription	Primary hematopoietic stem cells	blood
7	chr5:42972800-42985200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr5:42973200-42985600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr5:42975000-42984400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr5:42975200-42984400	Weak transcription	HSMM	muscle
11	chr5:42975200-42984400	Weak transcription	NH-A	brain
12	chr5:42975200-42985200	Weak transcription	Thymus	Thymus
13	chr5:42975200-42987600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr5:42975400-42985200	Weak transcription	Primary T cells from cord blood	blood
15	chr5:42978000-42985200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr5:42982200-42983400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr5:42982200-42986000	Strong transcription	Primary T cells fromperipheralblood	blood
18	chr5:42982200-42988000	Enhancers	HUVEC	blood vessel
19	chr5:42982400-42985400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr5:42982400-42986600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr5:42982600-42984400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:42982600-42985000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr5:42982600-42985000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr5:42982800-42983400	Enhancers	A549	lung
25	chr5:42982800-42983600	Enhancers	K562	blood
26	chr5:42982800-42983800	Weak transcription	HMEC	breast
27	chr5:42982800-42984400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr5:42982800-42984400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr5:42982800-42985000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr5:42982800-42985200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr5:42982800-42985400	Weak transcription	HSMMtube	muscle
32	chr5:42982800-42987600	Weak transcription	Dnd41	blood
33	chr5:42982800-42989400	Weak transcription	Adipose Nuclei	Adipose
34	chr5:42982800-42990800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:42983000-42984400	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr5:42983000-42984400	Weak transcription	NHDF-Ad	bronchial
37	chr5:42983000-42984400	Weak transcription	NHLF	lung
38	chr5:42983000-42985200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr5:42983000-42985600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr5:42983000-42990000	Weak transcription	Fetal Thymus	thymus
41	chr5:42983200-42983600	Weak transcription	NHEK	skin
42	chr5:42983200-42986000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr5:42983200-42986200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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