Variant report

Variant	rs2656069
Chromosome Location	chr15:78745707-78745708
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:78740565..78742425-chr15:78743943..78746196,2	MCF-7	breast:
2	chr15:78729183..78733288-chr15:78740820..78746070,7	K562	blood:
3	chr15:78742068..78744487-chr15:78745696..78748456,2	K562	blood:
4	chr15:78742068..78744005-chr15:78744591..78747196,2	K562	blood:
5	chr15:78731552..78733950-chr15:78743733..78745911,2	MCF-7	breast:
6	chr15:78727207..78732074-chr15:78744204..78747986,5	MCF-7	breast:
7	chr15:78743131..78746223-chr15:78751883..78753767,3	K562	blood:

Variant related genes	Relation type
ENSG00000136381	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10851906	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11072763	0.89[EUR][1000 genomes]
rs11072766	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12101809	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12442456	0.81[ASN][1000 genomes]
rs16969894	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2036529	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2036533	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2568483	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2568488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2568490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568493	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2568497	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2568498	0.81[CHB][hapmap];0.81[CHD][hapmap];0.89[JPT][hapmap];0.81[YRI][hapmap]
rs2568499	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2656055	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2656056	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2656070	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2656071	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656072	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2656073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2656074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28480606	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28511883	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28602670	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2869032	0.94[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2869045	1.00[ASW][hapmap];0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2915695	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938671	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2938674	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2958719	0.85[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]
rs35031105	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4887053	0.80[ASW][hapmap];0.94[CEU][hapmap];0.92[CHD][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs5019044	1.00[CEU][hapmap]
rs7174190	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7174348	0.86[EUR][1000 genomes]
rs924840	0.80[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs958025	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9672608	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9788682	0.82[CEU][hapmap]

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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
3	nsv833063	chr15:78605215-78754945	Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	esv1806890	chr15:78744695-78786064	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2656069	COX5A	cis	parietal	SCAN
rs2656069	FAH	cis	parietal	SCAN
rs2656069	PSMA4	cis	parietal	SCAN
rs2656069	PARP6	cis	cerebellum	SCAN
rs2656069	IREB2	cis	lesional skin	skin_eQTL
rs2656069	CHRNA5	cis	cerebellum	SCAN
rs2656069	IREB2	Cis_1M	lymphoblastoid	RTeQTL
rs2656069	PSMA4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78731600-78756400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78731600-78760200	Weak transcription	Aorta	Aorta
3	chr15:78732200-78747600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:78732200-78799400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:78732800-78758600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr15:78734000-78747200	Weak transcription	Fetal Brain Male	brain
7	chr15:78738600-78747400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:78738800-78747400	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:78739200-78747600	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr15:78739200-78748400	Weak transcription	HSMM	muscle
11	chr15:78739200-78748800	Weak transcription	HUVEC	blood vessel
12	chr15:78739200-78749600	Weak transcription	HSMMtube	muscle
13	chr15:78739200-78755200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr15:78739400-78747600	Weak transcription	NHDF-Ad	bronchial
15	chr15:78739400-78747800	Weak transcription	Osteobl	bone
16	chr15:78739600-78746800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:78739600-78755200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:78740000-78746600	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr15:78740400-78753200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr15:78740600-78748800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:78740600-78756000	Weak transcription	Brain Germinal Matrix	brain
22	chr15:78740800-78748200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:78741000-78747600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:78741200-78747000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:78741200-78747000	Weak transcription	Fetal Muscle Leg	muscle
26	chr15:78741200-78755400	Weak transcription	Fetal Stomach	stomach
27	chr15:78741200-78781800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:78741800-78746600	Weak transcription	Brain Hippocampus Middle	brain
29	chr15:78741800-78747400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr15:78742000-78747200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr15:78742000-78747200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:78742000-78747600	Weak transcription	Fetal Lung	lung
33	chr15:78742000-78749000	Weak transcription	NH-A	brain
34	chr15:78742000-78753000	Weak transcription	Dnd41	blood
35	chr15:78742000-78753400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr15:78742200-78747000	Weak transcription	Fetal Thymus	thymus
37	chr15:78742200-78748200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr15:78742400-78747200	Weak transcription	Fetal Heart	heart
39	chr15:78742400-78747400	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:78742600-78750400	Weak transcription	HepG2	liver
41	chr15:78742800-78746000	Weak transcription	Rectal Smooth Muscle	rectum
42	chr15:78742800-78747400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr15:78742800-78747400	Weak transcription	NHLF	lung
44	chr15:78742800-78747600	Weak transcription	Brain Anterior Caudate	brain
45	chr15:78742800-78753200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:78743000-78745800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:78743000-78747200	Weak transcription	Hela-S3	cervix
48	chr15:78743000-78747400	Weak transcription	Brain Substantia Nigra	brain
49	chr15:78743000-78747600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:78743000-78749200	Weak transcription	NHEK	skin

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