Variant report

Variant	rs12573992
Chromosome Location	chr11:67197757-67197758
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:67197430-67197921	GM12891	blood:	n/a	n/a
2	POLR2A	chr11:67197757-67197870	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr11:67197559-67209128	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:67194364..67200337-chr11:67272800..67277654,9	MCF-7	breast:
2	chr11:67195686..67198461-chr11:67271538..67273445,2	K562	blood:
3	chr11:67195659..67197780-chr5:130970138..130971644,2	MCF-7	breast:

Variant related genes	Relation type
RPS6KB2	TF binding region
ENSG00000110697	Chromatin interaction
ENSG00000167797	Chromatin interaction
ENSG00000158987	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10274	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11227793	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11601325	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12787021	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13859	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1476792	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1628442	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1638555	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1638556	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1638557	0.87[EUR][1000 genomes]
rs1638565	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1638588	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790752	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790753	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1790761	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1808279	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1893973	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2109123	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2302264	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35787427	0.86[EUR][1000 genomes]
rs36089024	0.87[EUR][1000 genomes]
rs3741168	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4930427	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs595130	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61889868	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs630172	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7110021	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7114510	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7131041	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7479801	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs869736	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs872375	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs917570	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531397	chr11:66653381-67465721	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	271 gene(s)	inside rSNPs	diseases
2	nsv897797	chr11:67023040-67293234	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	206 gene(s)	inside rSNPs	diseases
3	nsv1043037	chr11:67027193-67357425	Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	213 gene(s)	inside rSNPs	diseases
4	nsv897801	chr11:67033076-67432479	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
5	nsv1048230	chr11:67058231-67252397	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
6	nsv897804	chr11:67090571-67224278	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv1039205	chr11:67135246-67252397	Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Weak 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	122 gene(s)	inside rSNPs	diseases
8	esv1818769	chr11:67138811-67300457	Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
9	esv1798859	chr11:67139954-67272983	Active TSS Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
10	nsv897805	chr11:67155210-67283891	ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
11	nsv897806	chr11:67155210-67294308	Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
12	nsv897807	chr11:67155210-67414492	Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
13	nsv897808	chr11:67155210-67419855	Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	176 gene(s)	inside rSNPs	diseases
14	nsv897809	chr11:67156875-67276235	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
15	nsv555254	chr11:67164495-67288594	Weak transcription Flanking Active TSS Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	146 gene(s)	inside rSNPs	diseases
16	nsv534229	chr11:67164667-67411909	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
17	nsv897811	chr11:67166984-67218909	Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
18	nsv897812	chr11:67174597-67198887	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
19	nsv897813	chr11:67175692-67283891	Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
20	nsv521723	chr11:67175692-67311258	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
21	esv1847460	chr11:67182600-67219337	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
22	nsv524096	chr11:67186000-67224988	Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
23	nsv468604	chr11:67186000-67283891	Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
24	nsv555256	chr11:67186000-67283891	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12573992	PTPRCAP	cis	Esophagus Muscularis	GTEx
rs12573992	PTPRCAP	cis	Adipose Subcutaneous	GTEx
rs12573992	PTPRCAP	cis	Nerve Tibial	GTEx
rs12573992	PTPRCAP	cis	Skin Sun Exposed Lower leg	GTEx
rs12573992	PTPRCAP	cis	Artery Tibial	GTEx
rs12573992	AP003419.16	cis	Heart Left Ventricle	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:67196600-67198400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr11:67196800-67197800	Weak transcription	Ovary	ovary
3	chr11:67196800-67197800	Genic enhancers	Spleen	Spleen
4	chr11:67196800-67198400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr11:67196800-67198800	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr11:67196800-67199200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr11:67196800-67199200	Weak transcription	Aorta	Aorta
8	chr11:67196800-67210200	Weak transcription	Fetal Kidney	kidney
9	chr11:67197000-67197800	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:67197000-67197800	Enhancers	Primary T cells from cord blood	blood
11	chr11:67197000-67198000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr11:67197000-67198200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr11:67197000-67198400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:67197000-67198800	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr11:67197000-67198800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr11:67197000-67199800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr11:67197000-67201000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:67197000-67201400	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr11:67197000-67202400	Genic enhancers	Fetal Thymus	thymus
20	chr11:67197000-67202800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr11:67197200-67197800	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr11:67197200-67197800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr11:67197200-67197800	Enhancers	Liver	Liver
24	chr11:67197200-67197800	Enhancers	Colonic Mucosa	Colon
25	chr11:67197200-67197800	Weak transcription	Esophagus	oesophagus
26	chr11:67197200-67197800	Genic enhancers	Rectal Mucosa Donor 29	rectum
27	chr11:67197200-67197800	Weak transcription	K562	blood
28	chr11:67197200-67198000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr11:67197200-67198000	Genic enhancers	Stomach Smooth Muscle	stomach
30	chr11:67197200-67198200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:67197200-67198200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr11:67197200-67198200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:67197200-67198200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
34	chr11:67197200-67198200	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr11:67197200-67198200	Weak transcription	Brain Anterior Caudate	brain
36	chr11:67197200-67198200	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr11:67197200-67198200	Weak transcription	Brain Substantia Nigra	brain
38	chr11:67197200-67198200	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr11:67197200-67198200	Weak transcription	Left Ventricle	heart
40	chr11:67197200-67198200	Weak transcription	A549	lung
41	chr11:67197200-67198200	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr11:67197200-67198200	Weak transcription	NHLF	lung
43	chr11:67197200-67198400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr11:67197200-67198400	Weak transcription	Osteobl	bone
45	chr11:67197200-67198800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr11:67197200-67198800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr11:67197200-67198800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr11:67197200-67198800	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr11:67197200-67198800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr11:67197200-67198800	Weak transcription	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links