Variant report

Variant	rs11072765
Chromosome Location	chr15:78734292-78734293
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	chr15:78732279..78734656-chr15:78753816..78756332,3	MCF-7	breast:
2	chr15:78733161..78735105-chr15:78831790..78834378,2	K562	blood:

Variant related genes	Relation type
ENSG00000041357	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10519198	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11072762	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11639224	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12899131	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12909921	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12910090	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1847529	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2036532	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2568498	0.93[EUR][1000 genomes]
rs2568500	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2656058	0.93[EUR][1000 genomes]
rs2869046	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4390557	0.89[EUR][1000 genomes]
rs4436747	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8041628	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs954144	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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	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

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs11072765	CHRNA5	cis	Muscle Skeletal	GTEx
rs11072765	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs11072765	CHRNA5	cis	Nerve Tibial	GTEx
rs11072765	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs11072765	CHRNA5	cis	Heart Left Ventricle	GTEx
rs11072765	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs11072765	RP11-650L12.2	cis	lung	GTEx
rs11072765	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs11072765	RP11-650L12.2	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78731400-78734400	Weak transcription	Spleen	Spleen
2	chr15:78731400-78745400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:78731600-78734400	Weak transcription	Ovary	ovary
4	chr15:78731600-78734400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr15:78731600-78736800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr15:78731600-78740600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:78731600-78742800	Weak transcription	Esophagus	oesophagus
8	chr15:78731600-78742800	Weak transcription	Right Ventricle	heart
9	chr15:78731600-78756400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:78731600-78760200	Weak transcription	Aorta	Aorta
11	chr15:78731800-78738200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:78731800-78738200	Weak transcription	Colonic Mucosa	Colon
13	chr15:78731800-78740400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr15:78731800-78740800	Weak transcription	Stomach Mucosa	stomach
15	chr15:78732000-78735000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
16	chr15:78732000-78735200	Genic enhancers	Fetal Lung	lung
17	chr15:78732000-78736000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:78732200-78734400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr15:78732200-78734600	Genic enhancers	Rectal Mucosa Donor 29	rectum
20	chr15:78732200-78734800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr15:78732200-78734800	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr15:78732200-78734800	Weak transcription	NHLF	lung
23	chr15:78732200-78735200	Genic enhancers	Primary T cells from cord blood	blood
24	chr15:78732200-78735800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:78732200-78735800	Genic enhancers	Fetal Intestine Large	intestine
26	chr15:78732200-78736000	Strong transcription	H1 Cell Line	embryonic stem cell
27	chr15:78732200-78737000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
28	chr15:78732200-78738400	Weak transcription	Brain Substantia Nigra	brain
29	chr15:78732200-78738800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
30	chr15:78732200-78739000	Strong transcription	Placenta	Placenta
31	chr15:78732200-78739600	Strong transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:78732200-78739800	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr15:78732200-78740400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr15:78732200-78740400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr15:78732200-78741800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr15:78732200-78742800	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr15:78732200-78747600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:78732200-78799400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr15:78732400-78735000	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:78732400-78735200	Strong transcription	HSMMtube	muscle
41	chr15:78732400-78735400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:78732400-78735800	Genic enhancers	Duodenum Mucosa	Duodenum
43	chr15:78732400-78739600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:78732400-78740200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:78732400-78740600	Strong transcription	Fetal Stomach	stomach
46	chr15:78732400-78740800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr15:78732400-78742800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr15:78732400-78744400	Weak transcription	Fetal Kidney	kidney
49	chr15:78732600-78734600	Weak transcription	Brain Cingulate Gyrus	brain
50	chr15:78732600-78735200	Genic enhancers	A549	lung

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