Variant report

Variant	rs441805
Chromosome Location	chr13:111274467-111274468
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:111211377..111214970-chr13:111273880..111276435,4	MCF-7	breast:
2	chr13:111248410..111250824-chr13:111273874..111275589,2	MCF-7	breast:
3	chr13:111272905..111274580-chr13:111366963..111368758,2	MCF-7	breast:
4	chr13:111265984..111270011-chr13:111270710..111274775,8	MCF-7	breast:
5	chr13:111265898..111273230-chr13:111273500..111281065,16	MCF-7	breast:
6	chr13:111271645..111274603-chr13:111290397..111292824,3	MCF-7	breast:
7	chr13:111266306..111273367-chr13:111274094..111280494,12	K562	blood:
8	chr13:111271154..111277326-chr13:111363993..111367812,9	K562	blood:

No data

Variant related genes	Relation type
ENSG00000153487	Chromatin interaction
ENSG00000213995	Chromatin interaction
ENSG00000139832	Chromatin interaction
ENSG00000134905	Chromatin interaction
ENSG00000255831	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs2765341	0.87[ASW][hapmap];0.89[LWK][hapmap];0.93[MKK][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes]
rs2765346	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2766501	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2986321	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs330542	0.86[AFR][1000 genomes]
rs330543	0.84[AFR][1000 genomes]
rs330544	0.86[AFR][1000 genomes]
rs330545	0.86[AFR][1000 genomes]
rs330547	0.86[AFR][1000 genomes]
rs330548	0.86[AFR][1000 genomes]
rs330549	0.86[AFR][1000 genomes]
rs330550	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.80[YRI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs330554	0.85[CHB][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs330556	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330558	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs330560	0.80[EUR][1000 genomes]
rs330563	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs330564	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs330566	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs330570	0.93[YRI][hapmap]
rs381033	0.81[EUR][1000 genomes]
rs392660	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs403908	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs424649	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs440771	0.88[AFR][1000 genomes]
rs61970485	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[JPT][hapmap];0.84[TSI][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7998306	0.84[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs441805	NM_018210	cis	multi-tissue	Pritchard
rs441805	CARKD	cis	Whole Blood	GTEx
rs441805	AL139385.1	cis	Muscle Skeletal	GTEx
rs441805	CARS2	cis	lymphoblastoid	seeQTL
rs441805	CARKD	cis	Liver	GTEx
rs441805	CARKD	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111269000-111277000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr13:111269000-111277600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr13:111269000-111287000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr13:111269200-111274600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr13:111269400-111274600	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr13:111269400-111274600	Weak transcription	Aorta	Aorta
7	chr13:111269400-111274800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr13:111269400-111275000	Weak transcription	Esophagus	oesophagus
9	chr13:111269400-111275000	Weak transcription	Gastric	stomach
10	chr13:111269400-111275000	Weak transcription	Spleen	Spleen
11	chr13:111269400-111275000	Weak transcription	A549	lung
12	chr13:111269400-111275200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr13:111269400-111286600	Weak transcription	Fetal Brain Male	brain
14	chr13:111269400-111287200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr13:111269600-111274600	Weak transcription	Primary B cells from cord blood	blood
16	chr13:111269600-111274600	Weak transcription	Primary B cells from peripheral blood	blood
17	chr13:111269600-111274800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr13:111269600-111275000	Weak transcription	Fetal Brain Female	brain
19	chr13:111269600-111275200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr13:111269600-111277200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr13:111269600-111279800	Weak transcription	Primary hematopoietic stem cells	blood
22	chr13:111270000-111274600	Weak transcription	Thymus	Thymus
23	chr13:111270200-111274600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr13:111270200-111274800	Weak transcription	Primary T cells from cord blood	blood
25	chr13:111270200-111274800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr13:111270200-111275000	Weak transcription	HSMMtube	muscle
27	chr13:111270400-111274600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr13:111270400-111274600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr13:111270400-111274600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr13:111270400-111274600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr13:111270400-111274600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr13:111270400-111274600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr13:111270400-111274600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr13:111270400-111274600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr13:111270400-111274600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr13:111270400-111274600	Weak transcription	Adipose Nuclei	Adipose
37	chr13:111270400-111274600	Weak transcription	Brain Angular Gyrus	brain
38	chr13:111270400-111274600	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr13:111270400-111274600	Weak transcription	Colonic Mucosa	Colon
40	chr13:111270400-111274600	Weak transcription	Fetal Lung	lung
41	chr13:111270400-111274600	Weak transcription	Fetal Muscle Leg	muscle
42	chr13:111270400-111274600	Weak transcription	Placenta	Placenta
43	chr13:111270400-111274600	Weak transcription	Fetal Thymus	thymus
44	chr13:111270400-111274600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr13:111270400-111274600	Weak transcription	HUVEC	blood vessel
46	chr13:111270400-111274800	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr13:111270400-111274800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
48	chr13:111270400-111274800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr13:111270400-111274800	Enhancers	Liver	Liver
50	chr13:111270400-111274800	Weak transcription	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links