Variant report

Variant	rs1535467
Chromosome Location	chr13:50206328-50206329
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50205655..50207787-chr13:50213059..50215226,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHF11-3	chr13:50206316-50206373	NONHSAT033758

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs1925743	0.93[ASN][1000 genomes]
rs3803185	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3969	0.92[ASN][1000 genomes]
rs4415919	0.84[ASN][1000 genomes]
rs7322886	0.92[ASN][1000 genomes]
rs7981043	0.92[ASN][1000 genomes]
rs9526582	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535267	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9535277	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	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	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
7	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
rs1535467	ARL11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50200400-50209800	Weak transcription	Gastric	stomach
2	chr13:50202400-50210000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr13:50202800-50233600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr13:50203000-50209000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr13:50203000-50209000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr13:50203000-50209400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr13:50203200-50208800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr13:50203200-50209000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr13:50203200-50210600	Weak transcription	Small Intestine	intestine
10	chr13:50203200-50212200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr13:50203400-50209200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr13:50203600-50209800	Weak transcription	Primary T cells from cord blood	blood
13	chr13:50204000-50209200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr13:50204000-50209200	Weak transcription	Right Atrium	heart
15	chr13:50204000-50209800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr13:50204200-50209200	Weak transcription	Duodenum Mucosa	Duodenum
17	chr13:50204200-50209200	Weak transcription	Right Ventricle	heart
18	chr13:50204400-50206800	Genic enhancers	Primary monocytes fromperipheralblood	blood
19	chr13:50204600-50206800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr13:50204600-50206800	Weak transcription	K562	blood
21	chr13:50204600-50209000	Weak transcription	GM12878-XiMat	blood
22	chr13:50204600-50210000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr13:50204800-50206800	Weak transcription	Left Ventricle	heart
24	chr13:50204800-50207000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
25	chr13:50204800-50208400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr13:50205000-50207200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr13:50205000-50207400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr13:50205200-50207200	Weak transcription	HUVEC	blood vessel
29	chr13:50205200-50208800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr13:50205200-50209200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr13:50205200-50209200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr13:50205200-50209400	Weak transcription	Thymus	Thymus
33	chr13:50205200-50215400	Weak transcription	Esophagus	oesophagus
34	chr13:50205400-50209000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr13:50205400-50209000	Weak transcription	Fetal Thymus	thymus
36	chr13:50205400-50210000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
37	chr13:50205800-50210800	Enhancers	Fetal Heart	heart
38	chr13:50206000-50207200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr13:50206000-50209200	Weak transcription	Fetal Intestine Small	intestine
40	chr13:50206000-50209400	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr13:50206000-50211200	Genic enhancers	Primary B cells from cord blood	blood
42	chr13:50206200-50209000	Weak transcription	Lung	lung
43	chr13:50206200-50209200	Weak transcription	Spleen	Spleen

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