Variant report

Variant	rs1359542
Chromosome Location	chr13:50159073-50159074
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50140129..50142488-chr13:50158778..50160378,3	MCF-7	breast:
2	chr13:50068906..50071236-chr13:50159028..50161203,3	MCF-7	breast:
3	chr13:50016508..50019619-chr13:50158297..50162493,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136144	Chromatin interaction
ENSG00000136147	Chromatin interaction
ENSG00000102547	Chromatin interaction
ENSG00000136169	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1198421	0.98[ASN][1000 genomes]
rs1198422	0.98[ASN][1000 genomes]
rs1536192	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs1536195	0.86[EUR][1000 genomes]
rs1570883	0.86[EUR][1000 genomes]
rs1886793	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1998780	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1998781	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2104183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2146145	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2209506	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2274278	0.87[EUR][1000 genomes]
rs2274284	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2407697	0.85[EUR][1000 genomes]
rs2897741	0.81[EUR][1000 genomes]
rs3794376	0.86[EUR][1000 genomes]
rs4572288	0.90[ASN][1000 genomes]
rs4941648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4941650	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5007254	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6561539	0.83[EUR][1000 genomes]
rs6561540	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6561542	0.87[EUR][1000 genomes]
rs7139724	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7317140	0.83[EUR][1000 genomes]
rs7324024	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7983283	0.83[EUR][1000 genomes]
rs7986405	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7989286	0.87[EUR][1000 genomes]
rs7992691	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7994516	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7996012	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8000962	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9526577	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9535259	0.83[EUR][1000 genomes]
rs9535262	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9535269	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9596161	0.88[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	nsv1047311	chr13:49895019-50224227	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv916093	chr13:50050919-50290245	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1036135	chr13:50071310-50183103	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv541770	chr13:50071310-50183103	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv1054965	chr13:50102730-50251347	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv541771	chr13:50102730-50251347	Enhancers Active TSS Genic enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
7	esv2763020	chr13:50105055-50192259	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
8	nsv900071	chr13:50107289-50286218	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
9	nsv561616	chr13:50120435-50190246	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS 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	9 gene(s)	inside rSNPs	diseases
10	nsv949162	chr13:50120985-50195882	Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1046912	chr13:50122840-50189313	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
12	nsv1043902	chr13:50122840-50189999	Strong transcription Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
13	esv2761789	chr13:50122852-50185910	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
14	nsv455883	chr13:50124621-50185204	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
15	nsv561617	chr13:50124621-50185204	Genic enhancers Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
16	nsv1043697	chr13:50129199-50249241	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
17	esv2752657	chr13:50144995-50244150	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1359542	ARL11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50157800-50160200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr13:50157800-50160200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr13:50157800-50160400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr13:50158000-50159200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr13:50158000-50159200	Flanking Active TSS	Dnd41	blood
6	chr13:50158000-50160000	Active TSS	NHLF	lung
7	chr13:50158000-50160200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr13:50158000-50160200	Active TSS	Brain Germinal Matrix	brain
9	chr13:50158000-50160200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
10	chr13:50158000-50160600	Active TSS	Right Atrium	heart
11	chr13:50158200-50159200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
12	chr13:50158200-50160000	Active TSS	Muscle Satellite Cultured Cells	--
13	chr13:50158200-50160200	Active TSS	Brain Anterior Caudate	brain
14	chr13:50158200-50160200	Active TSS	NHDF-Ad	bronchial
15	chr13:50158200-50160400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:50158200-50160400	Active TSS	Brain Hippocampus Middle	brain
17	chr13:50158400-50159200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr13:50158400-50159200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr13:50158400-50159400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr13:50158400-50159400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr13:50158400-50159400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
22	chr13:50158400-50160000	Active TSS	HMEC	breast
23	chr13:50158400-50160200	Active TSS	Brain Cingulate Gyrus	brain
24	chr13:50158400-50160200	Active TSS	Thymus	Thymus
25	chr13:50158400-50160400	Active TSS	Fetal Kidney	kidney
26	chr13:50158400-50160600	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr13:50158400-50160600	Active TSS	Fetal Brain Female	brain
28	chr13:50158400-50160600	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr13:50158600-50159200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
30	chr13:50158600-50159200	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr13:50158600-50159200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr13:50158600-50159200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr13:50158600-50159200	Flanking Active TSS	Fetal Lung	lung
34	chr13:50158600-50159200	Flanking Active TSS	Fetal Thymus	thymus
35	chr13:50158600-50159200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr13:50158600-50159400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
37	chr13:50158600-50159400	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr13:50158600-50159400	Flanking Active TSS	Adipose Nuclei	Adipose
39	chr13:50158600-50159400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr13:50158600-50160000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr13:50158600-50160000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr13:50158600-50160000	Active TSS	Fetal Muscle Trunk	muscle
43	chr13:50158600-50160000	Active TSS	NH-A	brain
44	chr13:50158600-50160200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr13:50158600-50160200	Active TSS	Aorta	Aorta
46	chr13:50158600-50160200	Active TSS	Brain Angular Gyrus	brain
47	chr13:50158600-50160200	Active TSS	Psoas Muscle	Psoas
48	chr13:50158600-50160200	Active TSS	Right Ventricle	heart
49	chr13:50158600-50160200	Active TSS	HSMM	muscle
50	chr13:50158600-50160400	Active TSS	ES-WA7 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links