Variant report

Variant	rs1359541
Chromosome Location	chr13:50158939-50158940
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50018389..50020157-chr13:50156893..50158971,2	MCF-7	breast:
2	chr13:50140129..50142488-chr13:50158778..50160378,3	MCF-7	breast:
3	chr13:50157525..50159034-chr13:50176178..50177840,2	MCF-7	breast:
4	chr13:50016508..50019619-chr13:50158297..50162493,5	MCF-7	breast:

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

Extended variants
information (count: 51 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1359543	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1409015	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1925743	0.95[EUR][1000 genomes]
rs2094108	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2146144	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2146146	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3969	0.81[GIH][hapmap];0.82[JPT][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs4315259	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4409984	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4415919	0.87[EUR][1000 genomes]
rs4638463	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4942851	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4942854	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4942859	0.81[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4942860	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7322886	0.83[GIH][hapmap];0.82[JPT][hapmap];0.84[MKK][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs7322971	0.88[JPT][hapmap]
rs7329454	0.84[ASN][1000 genomes]
rs7334387	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7337571	0.89[JPT][hapmap]
rs7994201	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8000680	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9316462	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9316463	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9526580	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9526582	0.82[JPT][hapmap]
rs9535268	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535270	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535271	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9535275	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9535277	0.82[JPT][hapmap]
rs9568284	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568285	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9568286	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1359541	RNASEH2B	cis	parietal	SCAN
rs1359541	CAB39L	cis	cerebellum	SCAN
rs1359541	RCBTB1	cis	parietal	SCAN
rs1359541	RCBTB1	cis	cerebellum	SCAN
rs1359541	ARL11	cis	lymphoblastoid	seeQTL
rs1359541	ARL11	Cis_1M	lymphoblastoid	RTeQTL
rs1359541	ESD	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50139400-50159000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:50154200-50159000	Weak transcription	Gastric	stomach
3	chr13:50155200-50159000	Weak transcription	Pancreas	Pancrea
4	chr13:50156000-50159000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:50156000-50159000	Weak transcription	Spleen	Spleen
6	chr13:50157800-50160200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr13:50157800-50160200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr13:50157800-50160400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr13:50158000-50159000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:50158000-50159000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:50158000-50159000	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
12	chr13:50158000-50159000	Flanking Active TSS	NHEK	skin
13	chr13:50158000-50159200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr13:50158000-50159200	Flanking Active TSS	Dnd41	blood
15	chr13:50158000-50160000	Active TSS	NHLF	lung
16	chr13:50158000-50160200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr13:50158000-50160200	Active TSS	Brain Germinal Matrix	brain
18	chr13:50158000-50160200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr13:50158000-50160600	Active TSS	Right Atrium	heart
20	chr13:50158200-50159000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr13:50158200-50159000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr13:50158200-50159000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
23	chr13:50158200-50159200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
24	chr13:50158200-50160000	Active TSS	Muscle Satellite Cultured Cells	--
25	chr13:50158200-50160200	Active TSS	Brain Anterior Caudate	brain
26	chr13:50158200-50160200	Active TSS	NHDF-Ad	bronchial
27	chr13:50158200-50160400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr13:50158200-50160400	Active TSS	Brain Hippocampus Middle	brain
29	chr13:50158400-50159000	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr13:50158400-50159000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
31	chr13:50158400-50159000	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr13:50158400-50159000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr13:50158400-50159000	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr13:50158400-50159000	Flanking Active TSS	GM12878-XiMat	blood
35	chr13:50158400-50159000	Flanking Active TSS	HUVEC	blood vessel
36	chr13:50158400-50159200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
37	chr13:50158400-50159200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr13:50158400-50159400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr13:50158400-50159400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr13:50158400-50159400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr13:50158400-50160000	Active TSS	HMEC	breast
42	chr13:50158400-50160200	Active TSS	Brain Cingulate Gyrus	brain
43	chr13:50158400-50160200	Active TSS	Thymus	Thymus
44	chr13:50158400-50160400	Active TSS	Fetal Kidney	kidney
45	chr13:50158400-50160600	Active TSS	HUES48 Cell Line	embryonic stem cell
46	chr13:50158400-50160600	Active TSS	Fetal Brain Female	brain
47	chr13:50158400-50160600	Active TSS	Pancreatic Islets	Pancreatic Islet
48	chr13:50158600-50159000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr13:50158600-50159000	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr13:50158600-50159000	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell

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