Variant report

Variant	rs330549
Chromosome Location	chr13:111269277-111269278
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:111158551..111160525-chr13:111267801..111269585,2	MCF-7	breast:
2	chr13:111266587..111269692-chr13:111357018..111359356,4	K562	blood:
3	chr13:111265515..111270086-chr13:111364987..111368051,5	MCF-7	breast:
4	chr13:111268021..111270238-chr13:111291368..111294151,2	MCF-7	breast:
5	chr13:111268040..111269954-chr13:111270156..111273298,3	K562	blood:
6	chr13:111266965..111271727-chr13:111364973..111369025,9	MCF-7	breast:
7	chr13:111266746..111269387-chr13:111357064..111359748,3	MCF-7	breast:
8	chr13:111267467..111269967-chr13:111564590..111568374,3	MCF-7	breast:
9	chr13:111265756..111270693-chr13:111363417..111370660,10	K562	blood:
10	chr13:111267851..111270253-chr13:111566067..111568371,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134905	Chromatin interaction
ENSG00000255831	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000134871	Chromatin interaction
ENSG00000088448	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1043886	0.87[EUR][1000 genomes]
rs11551105	0.94[EUR][1000 genomes]
rs16940507	0.94[EUR][1000 genomes]
rs179356	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs191322	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2765341	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2986320	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs330542	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs330543	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs330544	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs330545	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs330546	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs330547	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs330548	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs330551	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs330557	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs330559	0.94[EUR][1000 genomes]
rs330569	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs330570	0.81[ASN][1000 genomes]
rs330572	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs371162	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3759463	0.94[EUR][1000 genomes]
rs379324	0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs380564	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs389541	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41275126	0.94[EUR][1000 genomes]
rs41275128	0.96[EUR][1000 genomes]
rs412822	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs422789	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs440771	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs441805	0.86[AFR][1000 genomes]
rs61969236	0.85[EUR][1000 genomes]
rs61970483	0.94[EUR][1000 genomes]
rs61970484	0.94[EUR][1000 genomes]
rs61970486	0.93[EUR][1000 genomes]
rs61970489	0.94[EUR][1000 genomes]
rs61970494	0.89[EUR][1000 genomes]
rs9559854	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
4	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
5	nsv901010	chr13:111165390-111286592	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking 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 lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv901011	chr13:111168951-111280002	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases
12	nsv901012	chr13:111220842-111340342	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv1038089	chr13:111229517-111274823	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
14	nsv1044340	chr13:111234073-111692994	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
15	nsv563123	chr13:111237260-111292044	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
16	nsv525124	chr13:111261267-111280002	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
17	nsv563124	chr13:111261267-111300943	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
18	nsv1048700	chr13:111265350-111658617	Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs330549	AL139385.1	cis	Whole Blood	GTEx
rs330549	CARKD	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111267200-111269400	Active TSS	A549	lung
2	chr13:111267200-111270000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr13:111267400-111269800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
4	chr13:111267600-111269400	Active TSS	H9 Cell Line	embryonic stem cell
5	chr13:111267600-111269400	Active TSS	Esophagus	oesophagus
6	chr13:111267600-111269400	Active TSS	Right Atrium	heart
7	chr13:111267800-111269400	Active TSS	HepG2	liver
8	chr13:111267800-111269600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:111267800-111270000	Active TSS	Ovary	ovary
10	chr13:111268000-111270000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr13:111268200-111269400	Flanking Active TSS	Primary hematopoietic stem cells	blood
12	chr13:111268400-111269400	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr13:111268400-111269400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr13:111268400-111269400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr13:111268400-111269400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr13:111268400-111269400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
17	chr13:111268400-111269400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr13:111268400-111269400	Flanking Active TSS	Adipose Nuclei	Adipose
19	chr13:111268400-111269400	Flanking Active TSS	Colonic Mucosa	Colon
20	chr13:111268400-111270400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr13:111268600-111269400	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr13:111268600-111269400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
23	chr13:111268600-111269400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr13:111268600-111269400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
25	chr13:111268600-111269400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
26	chr13:111268600-111269400	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr13:111268600-111269400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
28	chr13:111268600-111269400	Flanking Active TSS	Thymus	Thymus
29	chr13:111268600-111269400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr13:111268600-111269400	Flanking Active TSS	Osteobl	bone
31	chr13:111268600-111269600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
32	chr13:111268600-111269600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr13:111268600-111269800	Flanking Active TSS	Fetal Lung	lung
34	chr13:111268600-111270000	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr13:111268600-111270200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
36	chr13:111268600-111270400	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr13:111268800-111269400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
38	chr13:111268800-111269400	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
39	chr13:111268800-111269400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr13:111268800-111269400	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr13:111268800-111269400	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr13:111268800-111269400	Flanking Active TSS	Fetal Brain Male	brain
43	chr13:111268800-111269400	Flanking Active TSS	Fetal Brain Female	brain
44	chr13:111268800-111269400	Flanking Active TSS	Fetal Kidney	kidney
45	chr13:111268800-111269400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr13:111268800-111269400	Flanking Active TSS	HSMMtube	muscle
47	chr13:111268800-111269600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr13:111268800-111269600	Flanking Active TSS	Primary T cells from cord blood	blood
49	chr13:111268800-111269600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
50	chr13:111268800-111269600	Flanking Active TSS	Hela-S3	cervix

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