Variant report

Variant	rs10041063
Chromosome Location	chr5:80545341-80545342
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80543196..80546159-chr5:80550500..80552357,3	K562	blood:
2	chr5:80543196..80545536-chr5:80550500..80552357,2	K562	blood:

Variant related genes	Relation type
ENSG00000131730	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10036376	0.85[CEU][hapmap]
rs10038684	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10053706	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10055063	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10056565	0.83[ASN][1000 genomes]
rs10063615	0.83[ASN][1000 genomes]
rs10066296	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10073527	0.81[CEU][hapmap]
rs10078279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10474656	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514213	0.95[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514215	0.85[CEU][hapmap]
rs1055383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10942945	0.93[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11950033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12516414	0.81[CEU][hapmap]
rs13362314	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1566432	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16876403	0.81[CEU][hapmap]
rs17294418	0.95[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17294956	0.85[CEU][hapmap]
rs2270823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2270824	0.81[CEU][hapmap]
rs2406556	0.83[ASN][1000 genomes]
rs28464111	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28650401	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897389	0.94[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2897390	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703827	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704708	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704712	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704715	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704717	0.81[CEU][hapmap]
rs4704720	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs545	0.81[CEU][hapmap]
rs59132806	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60488995	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60904680	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61244991	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62365865	0.83[ASN][1000 genomes]
rs68077638	0.83[ASN][1000 genomes]
rs6866499	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6867884	0.83[ASN][1000 genomes]
rs6885028	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs6893467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73130869	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7381116	0.87[AMR][1000 genomes]
rs7448717	0.94[CEU][hapmap]
rs750728	0.85[CEU][hapmap]
rs7709071	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7709149	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs7720009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7728465	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7734902	1.00[CHB][hapmap];0.83[ASN][1000 genomes]
rs921928	1.00[CHB][hapmap]
rs9293841	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2763877	chr5:80535750-80545341	Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs10041063	CTC-281B15.1	cis	Stomach	GTEx
rs10041063	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs10041063	CTC-281B15.1	cis	Artery Aorta	GTEx
rs10041063	CTD-2248H3.1	cis	Artery Aorta	GTEx
rs10041063	CTC-281B15.1	cis	Artery Tibial	GTEx
rs10041063	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs10041063	CTD-2248H3.1	cis	Thyroid	GTEx
rs10041063	CTC-281B15.1	cis	Thyroid	GTEx
rs10041063	CTD-2248H3.1	cis	Esophagus Muscularis	GTEx
rs10041063	CTD-2248H3.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10041063	CTD-2248H3.1	cis	Adipose Subcutaneous	GTEx
rs10041063	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs10041063	CTD-2248H3.1	cis	lung	GTEx
rs10041063	CTD-2248H3.1	cis	Esophagus Mucosa	GTEx
rs10041063	CTC-281B15.1	cis	lung	GTEx
rs10041063	CKMT2	cis	normal skin	skin_eQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80527000-80546200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
3	chr5:80529400-80549400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr5:80529600-80545800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:80530000-80546400	Weak transcription	Primary hematopoietic stem cells	blood
6	chr5:80530800-80556400	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr5:80531200-80551200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr5:80531200-80556400	Weak transcription	Thymus	Thymus
9	chr5:80531200-80564200	Weak transcription	HepG2	liver
10	chr5:80531800-80555800	Weak transcription	Fetal Lung	lung
11	chr5:80532000-80548400	Weak transcription	Lung	lung
12	chr5:80532200-80548400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr5:80532200-80551000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr5:80532200-80556800	Weak transcription	Dnd41	blood
15	chr5:80536200-80547800	Weak transcription	Spleen	Spleen
16	chr5:80536200-80548600	Weak transcription	Fetal Intestine Small	intestine
17	chr5:80537800-80545400	Genic enhancers	Left Ventricle	heart
18	chr5:80538400-80551400	Weak transcription	GM12878-XiMat	blood
19	chr5:80539000-80555200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr5:80539200-80548400	Weak transcription	Gastric	stomach
21	chr5:80540200-80545400	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr5:80540800-80545400	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr5:80541400-80549200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr5:80541800-80550600	Weak transcription	Fetal Intestine Large	intestine
25	chr5:80541800-80564400	Weak transcription	A549	lung
26	chr5:80542200-80545600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr5:80542200-80557000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr5:80542400-80548600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr5:80542800-80546200	Weak transcription	Primary T cells from cord blood	blood
30	chr5:80542800-80546200	Weak transcription	Fetal Stomach	stomach
31	chr5:80542800-80548400	Weak transcription	Esophagus	oesophagus
32	chr5:80542800-80548800	Weak transcription	Fetal Muscle Trunk	muscle
33	chr5:80543000-80545400	Enhancers	Psoas Muscle	Psoas
34	chr5:80543000-80548400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr5:80543000-80554200	Weak transcription	Pancreas	Pancrea
36	chr5:80543400-80545800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr5:80543400-80546000	Weak transcription	Fetal Brain Female	brain
38	chr5:80543400-80547400	Weak transcription	Small Intestine	intestine
39	chr5:80543600-80546200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr5:80543600-80546200	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr5:80543600-80549000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr5:80543800-80565600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr5:80544000-80546400	Weak transcription	Fetal Muscle Leg	muscle
44	chr5:80544000-80549200	Weak transcription	NHEK	skin
45	chr5:80544000-80549400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:80544000-80557000	Weak transcription	Duodenum Mucosa	Duodenum
47	chr5:80544000-80564200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr5:80544000-80564400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr5:80544200-80546000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:80544200-80547800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links