Variant report

Variant	rs59549782
Chromosome Location	chr13:50193185-50193186
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50191955..50193680-chr13:50196033..50197758,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RCBTB1-1	chr13:50193066-50193334	NONHSAT033756

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11148155	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11616980	0.81[EUR][1000 genomes]
rs11618686	0.81[EUR][1000 genomes]
rs11619565	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12429350	0.81[ASN][1000 genomes]
rs12430463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56034850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56076648	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59934906	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61959865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61959868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61959873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61959906	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61959910	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61961440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73192614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73192638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9568274	0.81[EUR][1000 genomes]
rs9568281	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
4	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
5	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
6	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
7	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
8	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
rs59549782	ARL11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50181400-50194400	Weak transcription	Right Ventricle	heart
2	chr13:50190000-50194200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr13:50190200-50194400	Weak transcription	Left Ventricle	heart
4	chr13:50190200-50194400	Weak transcription	Spleen	Spleen
5	chr13:50190400-50194200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr13:50190400-50194400	Weak transcription	Brain Angular Gyrus	brain
7	chr13:50190400-50194400	Weak transcription	Brain Cingulate Gyrus	brain
8	chr13:50190600-50194200	Weak transcription	Right Atrium	heart
9	chr13:50190600-50194400	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr13:50190600-50195800	Weak transcription	Ovary	ovary
11	chr13:50190800-50193600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr13:50190800-50194000	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr13:50190800-50194400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr13:50190800-50194400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr13:50190800-50194400	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr13:50191000-50193200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr13:50191000-50194400	Weak transcription	Brain Germinal Matrix	brain
18	chr13:50191200-50194200	Weak transcription	NHDF-Ad	bronchial
19	chr13:50191200-50194400	Weak transcription	Adipose Nuclei	Adipose
20	chr13:50191200-50199400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr13:50191400-50193200	Weak transcription	Fetal Muscle Leg	muscle
22	chr13:50191400-50194400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr13:50191400-50194400	Enhancers	Fetal Thymus	thymus
24	chr13:50191600-50193200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr13:50191600-50194400	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr13:50191800-50194800	Enhancers	Primary hematopoietic stem cells	blood
27	chr13:50192000-50194400	Enhancers	Primary B cells from cord blood	blood
28	chr13:50192400-50194400	Weak transcription	Lung	lung
29	chr13:50192400-50196600	Weak transcription	Fetal Lung	lung
30	chr13:50192800-50193200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr13:50192800-50196600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr13:50193000-50193200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:50193000-50194200	Weak transcription	Fetal Heart	heart

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