Variant report

Variant	rs4943040
Chromosome Location	chr13:52493952-52493953
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:52493587..52494261-chr13:52503568..52504361,2	MCF-7	breast:
2	chr13:52493798..52494361-chr13:52503822..52504446,2	MCF-7	breast:
3	chr13:52480974..52481796-chr13:52493420..52494449,6	MCF-7	breast:
4	chr13:52492399..52494295-chr13:52701617..52703146,2	MCF-7	breast:
5	chr13:52493211..52494944-chr13:52498242..52500919,2	K562	blood:
6	chr13:52484875..52491698-chr13:52491732..52499779,14	MCF-7	breast:
7	chr13:52491156..52495004-chr13:52498889..52501522,3	MCF-7	breast:
8	chr13:52486706..52490426-chr13:52492535..52494617,3	K562	blood:
9	chr13:52484188..52486390-chr13:52491938..52494786,2	K562	blood:
10	chr13:52480324..52481830-chr13:52493649..52496094,2	MCF-7	breast:
11	chr13:52479905..52480672-chr13:52493409..52494046,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000232872	Chromatin interaction
ENSG00000197168	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12857062	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4941715	0.84[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9596613	0.84[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs9596615	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs967597	0.89[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	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv1044310	chr13:52321564-52643924	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	nsv1050117	chr13:52325116-52643924	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv934070	chr13:52362588-53174923	Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
6	nsv455888	chr13:52491193-52570728	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv561649	chr13:52491193-52570728	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4943040	NCRNA00282	cis	cerebellum	SCAN
rs4943040	CKAP2	cis	parietal	SCAN
rs4943040	THSD1	cis	cerebellum	SCAN
rs4943040	CKAP2	cis	cerebellum	SCAN
rs4943040	KCNRG	cis	parietal	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52464600-52494400	Weak transcription	Aorta	Aorta
2	chr13:52476400-52496600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr13:52480200-52497200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:52481200-52496400	Weak transcription	Stomach Smooth Muscle	stomach
5	chr13:52481200-52496600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr13:52481600-52502000	Weak transcription	Right Atrium	heart
7	chr13:52481800-52506000	Weak transcription	Ovary	ovary
8	chr13:52486400-52500200	Weak transcription	Fetal Kidney	kidney
9	chr13:52486400-52523400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr13:52486800-52502000	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr13:52487000-52507800	Weak transcription	Pancreas	Pancrea
12	chr13:52487400-52496800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr13:52488000-52507800	Weak transcription	Brain Anterior Caudate	brain
14	chr13:52488000-52508200	Weak transcription	Brain Angular Gyrus	brain
15	chr13:52488000-52508200	Weak transcription	Brain Hippocampus Middle	brain
16	chr13:52488200-52505800	Weak transcription	Brain Germinal Matrix	brain
17	chr13:52488200-52508000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr13:52488200-52542200	Weak transcription	Brain Cingulate Gyrus	brain
19	chr13:52488400-52496600	Weak transcription	Fetal Brain Female	brain
20	chr13:52488400-52496800	Weak transcription	Thymus	Thymus
21	chr13:52488600-52496400	Weak transcription	Fetal Stomach	stomach
22	chr13:52489000-52494600	Weak transcription	Esophagus	oesophagus
23	chr13:52489000-52496800	Weak transcription	Fetal Muscle Leg	muscle
24	chr13:52489600-52508400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr13:52490000-52509400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr13:52491200-52499800	Weak transcription	Fetal Heart	heart
27	chr13:52491200-52500200	Weak transcription	Lung	lung
28	chr13:52491600-52497000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr13:52491800-52495000	Weak transcription	Fetal Intestine Small	intestine
30	chr13:52492000-52508400	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr13:52492400-52496600	Weak transcription	Liver	Liver
32	chr13:52492400-52497000	Weak transcription	HepG2	liver
33	chr13:52492600-52539600	Weak transcription	Fetal Brain Male	brain
34	chr13:52493600-52494200	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr13:52493800-52494200	Enhancers	Fetal Intestine Large	intestine
36	chr13:52493800-52495200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr13:52493800-52496000	Enhancers	K562	blood
38	chr13:52493800-52496600	Enhancers	Placenta	Placenta

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