Variant report

Variant	rs4941715
Chromosome Location	chr13:52488543-52488544
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:52488313-52488591	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:52486992..52489143-chr13:52495004..52497139,2	K562	blood:
2	chr13:52486706..52490426-chr13:52492535..52494617,3	K562	blood:
3	chr13:52486431..52488974-chr13:52489616..52491490,2	MCF-7	breast:
4	chr13:52478878..52481837-chr13:52486558..52489316,5	MCF-7	breast:
5	chr13:52484875..52491698-chr13:52491732..52499779,14	MCF-7	breast:

No data

Variant related genes	Relation type
CTAGE3P	TF binding region

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12857062	0.87[ASN][1000 genomes]
rs4943040	0.84[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs9596613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9596615	0.86[ASN][1000 genomes]
rs967597	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4941715	LOC440138	cis	multi-tissue	Pritchard
rs4941715	ATP7B	cis	lymphoblastoid	seeQTL
rs4941715	KCNRG	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52464600-52494400	Weak transcription	Aorta	Aorta
2	chr13:52475600-52493800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:52476200-52493800	Weak transcription	K562	blood
4	chr13:52476400-52496600	Weak transcription	Duodenum Mucosa	Duodenum
5	chr13:52479400-52491000	Weak transcription	Fetal Intestine Large	intestine
6	chr13:52480200-52497200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr13:52481200-52496400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr13:52481200-52496600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr13:52481400-52491000	Weak transcription	Lung	lung
10	chr13:52481600-52502000	Weak transcription	Right Atrium	heart
11	chr13:52481800-52506000	Weak transcription	Ovary	ovary
12	chr13:52482000-52491000	Weak transcription	Liver	Liver
13	chr13:52485400-52489000	Enhancers	Esophagus	oesophagus
14	chr13:52486000-52488800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr13:52486000-52489000	Enhancers	Fetal Thymus	thymus
16	chr13:52486400-52500200	Weak transcription	Fetal Kidney	kidney
17	chr13:52486400-52523400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr13:52486600-52488800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr13:52486800-52489600	Weak transcription	Fetal Heart	heart
20	chr13:52486800-52502000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr13:52487000-52507800	Weak transcription	Pancreas	Pancrea
22	chr13:52487400-52496800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr13:52487600-52488800	Enhancers	Spleen	Spleen
24	chr13:52487600-52489000	Strong transcription	Fetal Intestine Small	intestine
25	chr13:52487600-52489000	Enhancers	Fetal Muscle Trunk	muscle
26	chr13:52487600-52489000	Enhancers	Fetal Muscle Leg	muscle
27	chr13:52487800-52489600	Strong transcription	HepG2	liver
28	chr13:52488000-52507800	Weak transcription	Brain Anterior Caudate	brain
29	chr13:52488000-52508200	Weak transcription	Brain Angular Gyrus	brain
30	chr13:52488000-52508200	Weak transcription	Brain Hippocampus Middle	brain
31	chr13:52488200-52505800	Weak transcription	Brain Germinal Matrix	brain
32	chr13:52488200-52508000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr13:52488200-52542200	Weak transcription	Brain Cingulate Gyrus	brain
34	chr13:52488400-52488600	Enhancers	H1 Cell Line	embryonic stem cell
35	chr13:52488400-52488600	Genic enhancers	Fetal Stomach	stomach
36	chr13:52488400-52496600	Weak transcription	Fetal Brain Female	brain
37	chr13:52488400-52496800	Weak transcription	Thymus	Thymus

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