Variant report

Variant	rs11169359
Chromosome Location	chr12:50691309-50691310
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50690840..50693744-chr12:50695723..50697728,2	MCF-7	breast:
2	chr12:50687536..50689810-chr12:50690498..50693200,2	MCF-7	breast:
3	chr12:50677314..50678874-chr12:50691066..50693797,2	MCF-7	breast:
4	chr12:50676871..50679447-chr12:50689934..50691681,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LARP4-3	chr12:50691304-50692152	NONHSAT028197

Variant related genes	Relation type
ENSG00000050405	Chromatin interaction
ENSG00000203427	Chromatin interaction
ENSG00000203430	Chromatin interaction
ENSG00000203433	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:141)

rs_ID	r²[population]
rs10467106	0.81[ASN][1000 genomes]
rs10506292	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10783344	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783349	0.90[EUR][1000 genomes]
rs10783350	0.88[EUR][1000 genomes]
rs10783352	0.80[ASN][1000 genomes]
rs10783353	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10876013	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876014	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876015	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876016	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876017	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10876018	0.88[EUR][1000 genomes]
rs10876023	0.88[ASN][1000 genomes]
rs10876028	0.87[ASN][1000 genomes]
rs11169314	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169315	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169317	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169319	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169322	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169331	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169332	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169335	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169339	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169345	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169347	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169348	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169349	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169350	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169351	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11169357	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169360	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11169367	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169369	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169370	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169371	0.90[EUR][1000 genomes]
rs11169373	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169374	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169375	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169376	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169377	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169379	0.88[EUR][1000 genomes]
rs11169386	0.87[EUR][1000 genomes]
rs11169390	0.88[ASN][1000 genomes]
rs11169391	0.87[ASN][1000 genomes]
rs11169395	0.87[ASN][1000 genomes]
rs11836169	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11838347	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12299669	0.83[ASN][1000 genomes]
rs12299758	0.87[ASN][1000 genomes]
rs12303082	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12312177	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12422417	0.88[ASN][1000 genomes]
rs12424691	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12424713	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12424876	0.87[ASN][1000 genomes]
rs12425229	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12425705	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12426444	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12811291	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12814094	0.88[ASN][1000 genomes]
rs12821454	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12821504	0.85[EUR][1000 genomes]
rs12823506	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12828340	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12832940	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1362983	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17124562	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1972611	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1984993	0.87[ASN][1000 genomes]
rs2009072	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2111988	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2302900	0.85[EUR][1000 genomes]
rs2358539	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28628775	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34039674	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34614542	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34825838	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34849043	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34858415	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34894919	0.89[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs35209607	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35535298	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35663729	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35768991	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35878271	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35933908	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs36017775	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs3812825	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3861100	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4348979	0.88[ASN][1000 genomes]
rs4421818	0.88[ASN][1000 genomes]
rs4445717	0.80[ASN][1000 genomes]
rs4768855	0.87[ASN][1000 genomes]
rs4768872	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768949	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4768951	0.87[EUR][1000 genomes]
rs6580730	0.80[ASN][1000 genomes]
rs6580735	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6580736	0.92[EUR][1000 genomes]
rs6580737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6580738	0.92[EUR][1000 genomes]
rs6580739	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6580740	0.89[EUR][1000 genomes]
rs6580741	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6580743	0.85[ASN][1000 genomes]
rs67138019	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7132551	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7135777	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71465002	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7295847	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7296291	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7301186	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7301189	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7302363	0.88[ASN][1000 genomes]
rs7304445	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7305995	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7308095	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7308885	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7310541	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7311378	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7311491	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7311973	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7312252	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7314465	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7315871	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7315955	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7399343	0.88[EUR][1000 genomes]
rs7485486	0.89[EUR][1000 genomes]
rs7486747	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7488682	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7489214	0.88[EUR][1000 genomes]
rs7953953	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7956468	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7972824	0.84[ASN][1000 genomes]
rs7974648	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7979830	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7980911	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9668187	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9705460	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9739363	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
2	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
3	esv2761738	chr12:50627292-50836427	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
4	nsv1035796	chr12:50634342-50784312	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
5	nsv702	chr12:50670870-50715934	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	nsv1053667	chr12:50679039-50801752	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
7	nsv1054480	chr12:50691039-50859665	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11169359	CERS5	cis	Nerve Tibial	GTEx
rs11169359	DIP2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50678000-50691600	Weak transcription	Gastric	stomach
2	chr12:50678000-50699800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr12:50678400-50696000	Weak transcription	HSMM	muscle
4	chr12:50678400-50708600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr12:50678600-50691800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr12:50678600-50695600	Weak transcription	Primary T cells fromperipheralblood	blood
7	chr12:50678600-50698800	Weak transcription	Pancreas	Pancrea
8	chr12:50678800-50691600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:50679000-50696200	Weak transcription	Osteobl	bone
10	chr12:50679800-50708600	Weak transcription	Liver	Liver
11	chr12:50680000-50691800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr12:50680200-50691800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr12:50686000-50699000	Weak transcription	Primary T cells from cord blood	blood
14	chr12:50686200-50691400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr12:50686600-50691600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr12:50686600-50691600	Weak transcription	Fetal Intestine Large	intestine
17	chr12:50686800-50696000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr12:50687000-50696600	Weak transcription	K562	blood
19	chr12:50687000-50705600	Weak transcription	HSMMtube	muscle
20	chr12:50689600-50692000	Weak transcription	Spleen	Spleen
21	chr12:50689600-50692200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr12:50689800-50691400	Weak transcription	Fetal Intestine Small	intestine
23	chr12:50689800-50692000	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr12:50689800-50692200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr12:50689800-50692200	Enhancers	NHEK	skin
26	chr12:50690000-50711800	Weak transcription	Ovary	ovary
27	chr12:50690400-50692200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:50690400-50692400	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr12:50690600-50691600	Weak transcription	Small Intestine	intestine
30	chr12:50690600-50691800	Enhancers	Stomach Mucosa	stomach
31	chr12:50690600-50692000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:50690800-50692200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr12:50691000-50691600	Enhancers	HUVEC	blood vessel
34	chr12:50691000-50692400	Enhancers	Adipose Nuclei	Adipose
35	chr12:50691000-50692400	Enhancers	Rectal Mucosa Donor 31	rectum
36	chr12:50691200-50691400	Enhancers	Lung	lung
37	chr12:50691200-50692000	Enhancers	Left Ventricle	heart
38	chr12:50691200-50696000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:50691200-50696600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr12:50691200-50696600	Weak transcription	A549	lung

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