Variant report

Variant	rs783543
Chromosome Location	chr15:83239486-83239487
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:83237529..83239820-chr15:83240454..83244037,3	MCF-7	breast:
2	chr15:83238387..83241317-chr15:83241503..83245353,3	K562	blood:

Variant related genes	Relation type
ENSG00000214575	Chromatin interaction

Extended variants
information (count: 98 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10152286	0.93[YRI][hapmap]
rs10163167	1.00[YRI][hapmap]
rs10400906	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs10468217	0.91[ASN][1000 genomes]
rs10906984	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs1145172	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1145173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11631963	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs11633829	0.91[CHB][hapmap];0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs11635624	0.95[CHB][hapmap];0.83[JPT][hapmap]
rs11637433	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs11855735	1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs12148332	0.89[ASN][1000 genomes]
rs12324877	0.86[YRI][hapmap]
rs12438312	0.81[ASN][1000 genomes]
rs12438371	0.93[YRI][hapmap]
rs12441776	0.93[YRI][hapmap]
rs1259180	0.93[ASN][1000 genomes]
rs1259182	0.85[ASN][1000 genomes]
rs1259183	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs1267657	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs1267658	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1267659	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs1269134	0.84[ASN][1000 genomes]
rs12916980	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1313492	0.88[ASN][1000 genomes]
rs1313493	0.88[ASN][1000 genomes]
rs1367841	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1594511	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs17158390	0.85[ASN][1000 genomes]
rs17158391	0.80[YRI][hapmap]
rs1864699	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2099259	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs2278355	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs2567635	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2567636	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2678445	0.89[ASN][1000 genomes]
rs2678448	0.89[ASN][1000 genomes]
rs28374463	0.81[ASN][1000 genomes]
rs28415133	0.88[ASN][1000 genomes]
rs2870965	0.96[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs2870966	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs28808991	0.90[ASN][1000 genomes]
rs34186444	0.85[ASN][1000 genomes]
rs35934048	0.89[ASN][1000 genomes]
rs36109438	0.88[ASN][1000 genomes]
rs3970696	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4778686	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4779032	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[ASN][1000 genomes]
rs4779039	0.96[CHB][hapmap];0.83[JPT][hapmap]
rs4779041	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs4779044	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs4779050	0.95[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs55924160	0.85[ASN][1000 genomes]
rs57181760	0.84[ASN][1000 genomes]
rs6603033	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs698500	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7165125	0.83[ASN][1000 genomes]
rs7167880	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs7171180	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7178350	0.82[ASN][1000 genomes]
rs7181761	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs7182403	0.84[ASN][1000 genomes]
rs7183881	0.84[ASN][1000 genomes]
rs7494860	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7496954	0.84[ASN][1000 genomes]
rs783520	0.84[ASN][1000 genomes]
rs783521	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs783522	0.85[ASN][1000 genomes]
rs783523	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs783525	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs783526	1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs783527	1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs783529	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs783530	0.89[ASN][1000 genomes]
rs783531	0.92[ASN][1000 genomes]
rs783532	0.91[ASN][1000 genomes]
rs783533	0.90[ASN][1000 genomes]
rs783534	0.90[ASN][1000 genomes]
rs783535	0.87[ASN][1000 genomes]
rs783536	0.90[ASN][1000 genomes]
rs783537	0.87[ASN][1000 genomes]
rs783539	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs783540	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs783545	0.94[ASN][1000 genomes]
rs803687	0.86[ASN][1000 genomes]
rs803688	0.88[ASN][1000 genomes]
rs803747	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs8040293	0.82[ASN][1000 genomes]
rs8043401	1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs9652567	0.94[CHB][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427965	chr15:82741381-83310525	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv428309	chr15:82741381-83310525	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv2758391	chr15:82879646-83310525	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	esv2760046	chr15:82879646-83310525	Strong transcription Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv1035899	chr15:83108446-83315731	Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833071	chr15:83123646-83310510	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv1054171	chr15:83237514-83468077	Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs783543	LOC283726	cis	multi-tissue	Pritchard
rs783543	FAM154B	cis	temporal cortex	BrainEAC

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:83219800-83239800	Weak transcription	Duodenum Smooth Muscle	Duodenum
2	chr15:83222600-83239600	Weak transcription	Ovary	ovary
3	chr15:83222600-83239600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:83222800-83240600	Weak transcription	Aorta	Aorta
5	chr15:83223800-83239600	Weak transcription	Brain Substantia Nigra	brain
6	chr15:83224800-83239800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr15:83232600-83239600	Weak transcription	Fetal Lung	lung
8	chr15:83234400-83239800	Weak transcription	HSMMtube	muscle
9	chr15:83234600-83239600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr15:83234600-83239800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr15:83234600-83239800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr15:83234800-83239600	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr15:83235800-83239600	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:83236000-83239600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr15:83236000-83239600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr15:83236000-83239600	Weak transcription	NH-A	brain
17	chr15:83236000-83243600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:83237200-83239600	Active TSS	Brain Angular Gyrus	brain
19	chr15:83237600-83239600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr15:83237600-83239800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr15:83238000-83239600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:83238000-83239800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr15:83238000-83239800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:83238600-83239600	Enhancers	NHDF-Ad	bronchial
25	chr15:83238600-83239600	Enhancers	Osteobl	bone
26	chr15:83238800-83240000	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr15:83239200-83239800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr15:83239200-83239800	Enhancers	Muscle Satellite Cultured Cells	--
29	chr15:83239200-83239800	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr15:83239200-83239800	Strong transcription	K562	blood
31	chr15:83239200-83240000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:83239200-83240200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:83239400-83239600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
34	chr15:83239400-83239600	Flanking Active TSS	Brain Anterior Caudate	brain
35	chr15:83239400-83239800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:83239400-83239800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr15:83239400-83239800	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr15:83239400-83239800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
39	chr15:83239400-83239800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:83239400-83239800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:83239400-83239800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:83239400-83239800	Enhancers	Brain Germinal Matrix	brain
43	chr15:83239400-83239800	Enhancers	Fetal Stomach	stomach
44	chr15:83239400-83239800	Enhancers	HSMM	muscle
45	chr15:83239400-83240000	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr15:83239400-83240000	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr15:83239400-83240200	Flanking Active TSS	Brain Cingulate Gyrus	brain
48	chr15:83239400-83240200	Flanking Active TSS	Brain Hippocampus Middle	brain
49	chr15:83239400-83240200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
50	chr15:83239400-83240200	Flanking Active TSS	Colon Smooth Muscle	Colon

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links