Variant report

Variant	rs330546
Chromosome Location	chr13:111270762-111270763
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:111270726..111272560-chr13:111277400..111279622,2	MCF-7	breast:
2	chr13:111270127..111273388-chr13:111363315..111367711,4	MCF-7	breast:
3	chr13:111268040..111269954-chr13:111270156..111273298,3	K562	blood:
4	chr13:111270148..111271814-chr13:111272109..111273731,2	K562	blood:
5	chr13:111265984..111270011-chr13:111270710..111274775,8	MCF-7	breast:
6	chr13:111266965..111271727-chr13:111364973..111369025,9	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134905	Chromatin interaction
ENSG00000213995	Chromatin interaction
ENSG00000153487	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1043886	0.88[EUR][1000 genomes]
rs11551105	0.95[EUR][1000 genomes]
rs16940507	0.95[EUR][1000 genomes]
rs179356	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs191322	0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2765341	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2765346	0.88[AFR][1000 genomes]
rs2766501	0.82[AFR][1000 genomes]
rs2986320	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2986321	0.80[AFR][1000 genomes]
rs330542	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330543	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330544	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330545	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330547	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330548	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330549	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs330551	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs330556	0.83[AFR][1000 genomes]
rs330557	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs330559	0.95[EUR][1000 genomes]
rs330569	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs330570	0.82[ASN][1000 genomes]
rs330572	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs371162	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759463	0.95[EUR][1000 genomes]
rs379324	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs380564	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs389541	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs392660	0.82[AFR][1000 genomes]
rs41275126	0.94[EUR][1000 genomes]
rs41275128	0.97[EUR][1000 genomes]
rs412822	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs422789	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs440771	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61969236	0.85[EUR][1000 genomes]
rs61970483	0.95[EUR][1000 genomes]
rs61970484	0.95[EUR][1000 genomes]
rs61970486	0.94[EUR][1000 genomes]
rs61970489	0.95[EUR][1000 genomes]
rs61970494	0.90[EUR][1000 genomes]
rs61970495	0.81[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
rs330546	CARKD	cis	Whole Blood	GTEx
rs330546	AL139385.1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111269000-111272200	Enhancers	Pancreas	Pancrea
2	chr13:111269000-111277000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr13:111269000-111277600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr13:111269000-111287000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:111269200-111271000	Enhancers	Primary T cells fromperipheralblood	blood
6	chr13:111269200-111271000	Enhancers	Fetal Stomach	stomach
7	chr13:111269200-111271400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr13:111269200-111271400	Enhancers	Stomach Mucosa	stomach
9	chr13:111269200-111274600	Weak transcription	Fetal Muscle Trunk	muscle
10	chr13:111269400-111270800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr13:111269400-111270800	Enhancers	Rectal Mucosa Donor 31	rectum
12	chr13:111269400-111270800	Enhancers	NHDF-Ad	bronchial
13	chr13:111269400-111271200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr13:111269400-111271200	Enhancers	Brain Anterior Caudate	brain
15	chr13:111269400-111271400	Enhancers	Fetal Intestine Small	intestine
16	chr13:111269400-111271400	Enhancers	Left Ventricle	heart
17	chr13:111269400-111271400	Enhancers	Psoas Muscle	Psoas
18	chr13:111269400-111271600	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr13:111269400-111271600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr13:111269400-111271600	Enhancers	Right Ventricle	heart
21	chr13:111269400-111271800	Enhancers	Rectal Smooth Muscle	rectum
22	chr13:111269400-111272000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr13:111269400-111274600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr13:111269400-111274600	Weak transcription	Aorta	Aorta
25	chr13:111269400-111274800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr13:111269400-111275000	Weak transcription	Esophagus	oesophagus
27	chr13:111269400-111275000	Weak transcription	Gastric	stomach
28	chr13:111269400-111275000	Weak transcription	Spleen	Spleen
29	chr13:111269400-111275000	Weak transcription	A549	lung
30	chr13:111269400-111275200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr13:111269400-111286600	Weak transcription	Fetal Brain Male	brain
32	chr13:111269400-111287200	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr13:111269600-111270800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr13:111269600-111271000	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr13:111269600-111271400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr13:111269600-111274600	Weak transcription	Primary B cells from cord blood	blood
37	chr13:111269600-111274600	Weak transcription	Primary B cells from peripheral blood	blood
38	chr13:111269600-111274800	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr13:111269600-111275000	Weak transcription	Fetal Brain Female	brain
40	chr13:111269600-111275200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr13:111269600-111277200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr13:111269600-111279800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr13:111269800-111270800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
44	chr13:111269800-111270800	Enhancers	Fetal Intestine Large	intestine
45	chr13:111269800-111271000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr13:111269800-111271600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr13:111269800-111274400	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr13:111270000-111270800	Enhancers	Osteobl	bone
49	chr13:111270000-111271000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr13:111270000-111271000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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