Variant report

Variant	rs10517686
Chromosome Location	chr4:159042629-159042630
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:159040586..159043659-chr4:159090356..159092814,3	MCF-7	breast:
2	chr4:159014385..159016745-chr4:159041064..159043729,3	MCF-7	breast:
3	chr4:159041667..159043431-chr4:159082269..159084157,2	MCF-7	breast:
4	chr4:159036873..159039591-chr4:159040527..159042688,2	MCF-7	breast:
5	chr4:159041377..159043283-chr4:159093182..159095252,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164125	Chromatin interaction
ENSG00000248429	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10021199	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10517685	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100152	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11933839	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11939690	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13130880	0.86[ASN][1000 genomes]
rs13137328	0.86[ASN][1000 genomes]
rs13137541	0.86[ASN][1000 genomes]
rs17036992	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036995	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17037201	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17037232	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17212066	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17212714	0.91[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17271385	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17279270	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2594759	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2594760	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2725492	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs2725504	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2725505	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2725506	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2725507	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2725508	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs2881374	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234916	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs4443327	0.86[ASN][1000 genomes]
rs4508943	1.00[CHB][hapmap]
rs4510503	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs4549446	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs4608853	0.86[ASN][1000 genomes]
rs6536289	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs6536290	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs6536294	0.86[ASN][1000 genomes]
rs6815974	0.86[ASN][1000 genomes]
rs6820988	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs6834839	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6837943	0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72691603	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72691606	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72691610	0.81[EUR][1000 genomes]
rs72691615	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691620	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691622	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691626	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691627	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691629	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691631	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691632	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691634	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691636	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72691649	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72695726	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72695736	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72695741	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72695744	0.90[EUR][1000 genomes]
rs72695745	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72695747	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72695748	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72695749	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72695750	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72695751	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72695753	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7664129	0.86[ASN][1000 genomes]
rs7678302	0.91[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9997618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993476	chr4:158550643-159202015	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv1030124	chr4:158758675-159251140	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv1021067	chr4:158972282-159175475	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv880293	chr4:159012365-159049020	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10517686	FLJ11155	cis	multi-tissue	Pritchard
rs10517686	TMEM144	cis	Esophagus Muscularis	GTEx
rs10517686	DKFZp434L142	cis	multi-tissue	Pritchard
rs10517686	RP11-597D13.9	cis	Esophagus Muscularis	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:159034200-159046200	Weak transcription	HUVEC	blood vessel
2	chr4:159041200-159043800	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr4:159041200-159043800	Enhancers	Fetal Stomach	stomach
4	chr4:159041400-159043000	Enhancers	Placenta Amnion	Placenta Amnion
5	chr4:159041400-159043000	Enhancers	Rectal Smooth Muscle	rectum
6	chr4:159041400-159044600	Enhancers	HSMM	muscle
7	chr4:159041600-159043800	Weak transcription	NHLF	lung
8	chr4:159041600-159044200	Enhancers	Fetal Lung	lung
9	chr4:159041800-159042800	Active TSS	Ovary	ovary
10	chr4:159042000-159042800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr4:159042000-159042800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr4:159042000-159042800	Enhancers	Fetal Heart	heart
13	chr4:159042000-159042800	Active TSS	Fetal Muscle Trunk	muscle
14	chr4:159042000-159042800	Enhancers	HepG2	liver
15	chr4:159042000-159042800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
16	chr4:159042000-159043000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr4:159042000-159043000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr4:159042000-159044400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr4:159042000-159046800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr4:159042200-159042800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:159042200-159048000	Weak transcription	Fetal Intestine Large	intestine
22	chr4:159042200-159051400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr4:159042400-159042800	Enhancers	Brain Angular Gyrus	brain
24	chr4:159042400-159042800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr4:159042400-159042800	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr4:159042400-159044000	Enhancers	Muscle Satellite Cultured Cells	--
27	chr4:159042400-159044200	Enhancers	Osteobl	bone
28	chr4:159042400-159044600	Enhancers	NHDF-Ad	bronchial
29	chr4:159042400-159050800	Weak transcription	Aorta	Aorta
30	chr4:159042600-159042800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr4:159042600-159042800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr4:159042600-159042800	Enhancers	Adipose Nuclei	Adipose
33	chr4:159042600-159042800	Enhancers	Brain Hippocampus Middle	brain
34	chr4:159042600-159042800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr4:159042600-159042800	Flanking Active TSS	Colon Smooth Muscle	Colon
36	chr4:159042600-159042800	Enhancers	Fetal Muscle Leg	muscle
37	chr4:159042600-159042800	Flanking Active TSS	Stomach Smooth Muscle	stomach
38	chr4:159042600-159042800	Enhancers	HMEC	breast
39	chr4:159042600-159042800	Flanking Active TSS	HSMMtube	muscle
40	chr4:159042600-159042800	Flanking Active TSS	NH-A	brain
41	chr4:159042600-159043000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:159042600-159043800	Weak transcription	Fetal Kidney	kidney
43	chr4:159042600-159044400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:159042600-159044600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr4:159042600-159053400	Weak transcription	Right Atrium	heart
46	chr4:159042600-159053600	Weak transcription	Brain Anterior Caudate	brain
47	chr4:159042600-159060200	Weak transcription	Brain Substantia Nigra	brain

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