Variant report

Variant	rs401084
Chromosome Location	chr13:111310086-111310087
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:111308870..111310970-chr13:111364817..111367512,2	MCF-7	breast:
2	chr13:111302128..111303846-chr13:111308672..111310987,2	K562	blood:
3	chr13:111304729..111307376-chr13:111307813..111310341,2	K562	blood:

Variant related genes	Relation type
ENSG00000153487	Chromatin interaction
ENSG00000134905	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11619800	0.82[ASN][1000 genomes]
rs1193458	0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2119480	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs369788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs376602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs378399	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs381835	0.83[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4000216	0.80[ASN][1000 genomes]
rs410049	0.96[YRI][hapmap]
rs418935	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs436462	0.96[CHB][hapmap];0.82[ASN][1000 genomes]
rs440500	0.97[YRI][hapmap]
rs453757	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4771705	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4773237	0.82[ASN][1000 genomes]
rs6492297	0.82[ASN][1000 genomes]
rs7317796	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7320005	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7491363	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7998328	0.95[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9515266	0.90[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs9515267	0.82[ASN][1000 genomes]
rs9521884	0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9521885	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9521890	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9645874	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv1042232	chr13:111282123-111348475	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
12	nsv901013	chr13:111291192-111340342	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
13	nsv901014	chr13:111302922-111380684	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	197 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs401084	AL139385.1	cis	Muscle Skeletal	GTEx
rs401084	CARKD	cis	Muscle Skeletal	GTEx
rs401084	CARS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111280800-111328600	Weak transcription	Psoas Muscle	Psoas
2	chr13:111287400-111310200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr13:111289400-111312000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr13:111293400-111314800	Weak transcription	HUVEC	blood vessel
5	chr13:111294000-111311800	Weak transcription	Fetal Kidney	kidney
6	chr13:111296000-111311600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr13:111296600-111311400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr13:111296800-111310200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr13:111297200-111310200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr13:111297200-111313800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr13:111297600-111314400	Strong transcription	Fetal Intestine Large	intestine
12	chr13:111297800-111310600	Strong transcription	Fetal Stomach	stomach
13	chr13:111297800-111311400	Strong transcription	Fetal Muscle Leg	muscle
14	chr13:111297800-111317200	Weak transcription	Colon Smooth Muscle	Colon
15	chr13:111297800-111336400	Weak transcription	Small Intestine	intestine
16	chr13:111298000-111310200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr13:111298000-111320400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr13:111301200-111315600	Weak transcription	K562	blood
19	chr13:111301200-111322800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr13:111301600-111311400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr13:111301600-111322800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr13:111301600-111324400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr13:111301800-111313600	Weak transcription	Fetal Brain Male	brain
24	chr13:111302000-111322800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr13:111302200-111351400	Weak transcription	Stomach Mucosa	stomach
26	chr13:111303200-111314000	Weak transcription	Right Ventricle	heart
27	chr13:111303200-111314400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr13:111303400-111310200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr13:111303400-111310200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr13:111303400-111314000	Weak transcription	Left Ventricle	heart
31	chr13:111303400-111314200	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr13:111303400-111315600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr13:111303400-111327800	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr13:111303600-111310200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr13:111303600-111312400	Weak transcription	Brain Angular Gyrus	brain
36	chr13:111303800-111310200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr13:111303800-111313800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr13:111304000-111311400	Weak transcription	NHDF-Ad	bronchial
39	chr13:111304000-111313400	Weak transcription	Brain Substantia Nigra	brain
40	chr13:111304400-111310200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr13:111304800-111310200	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr13:111304800-111311600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr13:111305000-111311400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr13:111305200-111317600	Weak transcription	Rectal Smooth Muscle	rectum
45	chr13:111305400-111310400	Weak transcription	Brain Germinal Matrix	brain
46	chr13:111305400-111314000	Weak transcription	Pancreas	Pancrea
47	chr13:111305800-111311200	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr13:111306000-111313400	Weak transcription	Brain Hippocampus Middle	brain
49	chr13:111306000-111313600	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr13:111306200-111311400	Weak transcription	HepG2	liver

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