Variant report

Variant	rs8041628
Chromosome Location	chr15:78735355-78735356
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78735160..78737788-chr15:78742563..78745375,2	MCF-7	breast:
2	chr15:78734814..78737530-chr15:78775565..78778054,2	K562	blood:

Variant related genes	Relation type
ENSG00000136381	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10519198	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11072762	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11072765	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11639224	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12899131	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12909921	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12910090	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16969899	0.85[LWK][hapmap]
rs1847529	1.00[CEU][hapmap];0.95[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];0.99[ASN][1000 genomes]
rs2036532	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2292116	0.88[LWK][hapmap]
rs2568498	1.00[CEU][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes]
rs2568500	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2656058	0.94[EUR][1000 genomes]
rs2869030	0.85[JPT][hapmap]
rs2869046	0.82[CHB][hapmap];0.85[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3743079	0.88[LWK][hapmap]
rs3817092	0.88[LWK][hapmap]
rs4390557	0.89[EUR][1000 genomes]
rs4436747	0.92[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs954144	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs8041628	IREB2	cis	multi-tissue	Pritchard
rs8041628	CHRNA5	cis	Adipose Subcutaneous	GTEx
rs8041628	IREB2	cis	cerebellum	SCAN
rs8041628	RP11-650L12.2	cis	Adipose Subcutaneous	GTEx
rs8041628	CHRNA5	cis	Heart Left Ventricle	GTEx
rs8041628	CHRNA5	cis	multi-tissue	Pritchard
rs8041628	RP11-650L12.2	cis	Heart Left Ventricle	GTEx
rs8041628	IREB2	cis	parietal	SCAN
rs8041628	RP11-650L12.2	cis	Muscle Skeletal	GTEx
rs8041628	UBE2Q2	cis	cerebellum	SCAN
rs8041628	CHRNA5	cis	Muscle Skeletal	GTEx
rs8041628	CHRNA5	cis	cerebellum	SCAN
rs8041628	RP11-650L12.2	cis	lung	GTEx
rs8041628	CHRNA5	cis	Nerve Tibial	GTEx
rs8041628	CHRNA5	cis	parietal	SCAN
rs8041628	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	chr15:78731400-78745400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr15:78731600-78736800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr15:78731600-78740600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:78731600-78742800	Weak transcription	Esophagus	oesophagus
5	chr15:78731600-78742800	Weak transcription	Right Ventricle	heart
6	chr15:78731600-78756400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr15:78731600-78760200	Weak transcription	Aorta	Aorta
8	chr15:78731800-78738200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr15:78731800-78738200	Weak transcription	Colonic Mucosa	Colon
10	chr15:78731800-78740400	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr15:78731800-78740800	Weak transcription	Stomach Mucosa	stomach
12	chr15:78732000-78736000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:78732200-78735800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:78732200-78735800	Genic enhancers	Fetal Intestine Large	intestine
15	chr15:78732200-78736000	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr15:78732200-78737000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
17	chr15:78732200-78738400	Weak transcription	Brain Substantia Nigra	brain
18	chr15:78732200-78738800	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr15:78732200-78739000	Strong transcription	Placenta	Placenta
20	chr15:78732200-78739600	Strong transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:78732200-78739800	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:78732200-78740400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:78732200-78740400	Strong transcription	Fetal Muscle Trunk	muscle
24	chr15:78732200-78741800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr15:78732200-78742800	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr15:78732200-78747600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:78732200-78799400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr15:78732400-78735400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:78732400-78735800	Genic enhancers	Duodenum Mucosa	Duodenum
30	chr15:78732400-78739600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:78732400-78740200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr15:78732400-78740600	Strong transcription	Fetal Stomach	stomach
33	chr15:78732400-78740800	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr15:78732400-78742800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:78732400-78744400	Weak transcription	Fetal Kidney	kidney
36	chr15:78732600-78739400	Strong transcription	Osteobl	bone
37	chr15:78732800-78736000	Genic enhancers	Adipose Nuclei	Adipose
38	chr15:78732800-78740000	Strong transcription	Primary B cells from peripheral blood	blood
39	chr15:78732800-78758600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:78733000-78735600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
41	chr15:78733200-78736000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:78733200-78737600	Strong transcription	NHDF-Ad	bronchial
43	chr15:78733200-78738000	Weak transcription	Psoas Muscle	Psoas
44	chr15:78733200-78739200	Strong transcription	NH-A	brain
45	chr15:78733200-78742200	Strong transcription	Fetal Thymus	thymus
46	chr15:78733400-78736800	Strong transcription	HUVEC	blood vessel
47	chr15:78733400-78738800	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr15:78733400-78740200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:78733400-78741000	Weak transcription	Fetal Heart	heart
50	chr15:78733400-78744000	Strong transcription	Primary B cells from cord blood	blood

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