Variant report

Variant	rs56076648
Chromosome Location	chr13:50180858-50180859
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50017613..50020080-chr13:50178535..50181318,2	MCF-7	breast:
2	chr13:49875023..49875959-chr13:50180755..50181847,8	K562	blood:
3	chr13:49919468..49922351-chr13:50179863..50182327,2	K562	blood:
4	chr13:50071647..50073472-chr13:50180377..50183221,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102547	Chromatin interaction
ENSG00000136169	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11148155	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11619565	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12429350	0.85[ASN][1000 genomes]
rs12430463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56034850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59549782	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61959873	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61959882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61959906	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61959910	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61961440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192614	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73192638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9568269	0.81[EUR][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
rs56076648	ARL11	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50176800-50181000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr13:50178200-50181000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr13:50179000-50181000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr13:50179000-50181000	Weak transcription	Fetal Lung	lung
5	chr13:50179200-50181000	Weak transcription	Fetal Intestine Small	intestine
6	chr13:50179200-50181000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr13:50179200-50181000	Weak transcription	Osteobl	bone
8	chr13:50179400-50181000	Weak transcription	GM12878-XiMat	blood
9	chr13:50179400-50181000	Enhancers	HepG2	liver
10	chr13:50179600-50181000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr13:50179800-50181000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr13:50179800-50181000	Weak transcription	Fetal Heart	heart
13	chr13:50180800-50181000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
14	chr13:50180800-50181000	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr13:50180800-50181000	Enhancers	Primary B cells from cord blood	blood
16	chr13:50180800-50181000	Enhancers	Primary T cells fromperipheralblood	blood
17	chr13:50180800-50181000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr13:50180800-50181000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr13:50180800-50181000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr13:50180800-50181000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr13:50180800-50181000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr13:50180800-50181000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr13:50180800-50181000	Enhancers	Colonic Mucosa	Colon
24	chr13:50180800-50181000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
25	chr13:50180800-50181000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr13:50180800-50181000	Enhancers	Dnd41	blood
27	chr13:50180800-50181000	Flanking Active TSS	K562	blood
28	chr13:50180800-50181200	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr13:50180800-50181400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr13:50180800-50181400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr13:50180800-50181400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:50180800-50181400	Active TSS	Primary T helper cells PMA-I stimulated	--
33	chr13:50180800-50181400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr13:50180800-50181400	Active TSS	Muscle Satellite Cultured Cells	--
35	chr13:50180800-50181400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr13:50180800-50181400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr13:50180800-50181400	Flanking Active TSS	Adipose Nuclei	Adipose
38	chr13:50180800-50181400	Active TSS	Brain Cingulate Gyrus	brain
39	chr13:50180800-50181400	Active TSS	Brain Substantia Nigra	brain
40	chr13:50180800-50181400	Active TSS	Duodenum Mucosa	Duodenum
41	chr13:50180800-50181400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
42	chr13:50180800-50181400	Active TSS	Pancreatic Islets	Pancreatic Islet
43	chr13:50180800-50181400	Active TSS	Ovary	ovary
44	chr13:50180800-50181400	Active TSS	Skeletal Muscle Male	skeletal muscle
45	chr13:50180800-50181400	Active TSS	Stomach Smooth Muscle	stomach
46	chr13:50180800-50181400	Active TSS	A549	lung
47	chr13:50180800-50181400	Active TSS	HSMM	muscle
48	chr13:50180800-50181400	Active TSS	Monocytes-CD14+_RO01746	blood
49	chr13:50180800-50181800	Enhancers	Fetal Thymus	thymus
50	chr13:50180800-50183200	Enhancers	Primary B cells from peripheral blood	blood

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