Variant report

Variant	rs17027280
Chromosome Location	chr2:86733287-86733288
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:86730870..86733454-chr2:86738287..86740838,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115561	Chromatin interaction

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs1030886	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1030887	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11127043	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11548929	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11890032	0.89[EUR][1000 genomes]
rs11891659	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11899532	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1437614	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1518808	0.91[EUR][1000 genomes]
rs1518810	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs1518812	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027265	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027270	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17027296	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34605051	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs34633268	0.91[EUR][1000 genomes]
rs55688177	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55708352	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55828608	0.91[EUR][1000 genomes]
rs56055358	0.89[EUR][1000 genomes]
rs56085540	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56169889	0.91[EUR][1000 genomes]
rs56211578	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56227180	0.81[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56242451	0.89[EUR][1000 genomes]
rs56347930	0.91[EUR][1000 genomes]
rs56378606	0.90[EUR][1000 genomes]
rs57291816	0.91[EUR][1000 genomes]
rs57836876	0.89[EUR][1000 genomes]
rs58091125	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58361202	0.91[EUR][1000 genomes]
rs58829418	0.89[EUR][1000 genomes]
rs59026369	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59183618	0.87[EUR][1000 genomes]
rs59255035	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59336972	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59521243	0.80[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs59613942	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59859947	0.96[EUR][1000 genomes]
rs59895355	0.96[EUR][1000 genomes]
rs60073472	0.83[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs60244636	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60304516	0.91[EUR][1000 genomes]
rs60717666	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60796561	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60810860	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs61028062	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61465748	0.96[EUR][1000 genomes]
rs61547860	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6710780	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6720414	0.96[EUR][1000 genomes]
rs6740863	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6745875	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72930315	0.91[EUR][1000 genomes]
rs72930323	0.91[EUR][1000 genomes]
rs72930336	0.91[EUR][1000 genomes]
rs72930340	0.91[EUR][1000 genomes]
rs72930349	0.91[EUR][1000 genomes]
rs72930361	0.91[EUR][1000 genomes]
rs72930362	0.91[EUR][1000 genomes]
rs72930364	0.91[EUR][1000 genomes]
rs72930369	0.91[EUR][1000 genomes]
rs72930387	0.89[EUR][1000 genomes]
rs72930396	0.87[EUR][1000 genomes]
rs72930400	0.87[EUR][1000 genomes]
rs72932307	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72932310	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932311	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932316	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932319	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72932336	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932350	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932358	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932364	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932369	0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72932380	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73949838	0.90[EUR][1000 genomes]
rs73949839	0.90[EUR][1000 genomes]
rs7562493	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7579234	0.87[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7585722	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7586028	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7604179	1.00[EUR][1000 genomes]
rs7608800	1.00[CEU][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs966477	0.83[LWK][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3412938	chr2:86370969-86867936	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
2	nsv532724	chr2:86622295-87086407	Weak transcription Active TSS Genic enhancers Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17027280	MRPL35	cis	parietal	SCAN
rs17027280	KRCC1	cis	cerebellum	SCAN
rs17027280	VPS24	Cis_1M	lymphoblastoid	RTeQTL
rs17027280	VPS24	cis	parietal	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:86679800-86757000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:86709200-86737400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
3	chr2:86719800-86734600	Weak transcription	Psoas Muscle	Psoas
4	chr2:86724600-86737800	Strong transcription	Stomach Smooth Muscle	stomach
5	chr2:86726400-86735400	Weak transcription	NHLF	lung
6	chr2:86726400-86737400	Weak transcription	HUVEC	blood vessel
7	chr2:86726400-86741800	Weak transcription	NH-A	brain
8	chr2:86726400-86753000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:86726600-86736400	Weak transcription	NHDF-Ad	bronchial
10	chr2:86726600-86748600	Weak transcription	Hela-S3	cervix
11	chr2:86726800-86739000	Weak transcription	K562	blood
12	chr2:86727000-86737200	Strong transcription	Rectal Mucosa Donor 31	rectum
13	chr2:86727400-86734400	Weak transcription	Fetal Heart	heart
14	chr2:86727600-86734600	Weak transcription	HMEC	breast
15	chr2:86728000-86734200	Weak transcription	HSMM	muscle
16	chr2:86728000-86737600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr2:86728000-86737600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:86728000-86737600	Strong transcription	Adipose Nuclei	Adipose
19	chr2:86728000-86737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr2:86728000-86737800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr2:86728000-86737800	Strong transcription	Fetal Intestine Large	intestine
22	chr2:86728000-86738000	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr2:86728000-86738400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr2:86728200-86737800	Strong transcription	Cortex derived primary cultured neurospheres	brain
25	chr2:86728200-86737800	Weak transcription	Stomach Mucosa	stomach
26	chr2:86728200-86738400	Strong transcription	Dnd41	blood
27	chr2:86728200-86755800	Weak transcription	Fetal Brain Male	brain
28	chr2:86728400-86736200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr2:86728400-86737800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:86728400-86738000	Strong transcription	Liver	Liver
31	chr2:86728400-86738400	Strong transcription	Primary T cells fromperipheralblood	blood
32	chr2:86728400-86738400	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr2:86728400-86738400	Strong transcription	A549	lung
34	chr2:86728400-86747200	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr2:86728600-86737600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr2:86728600-86738200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:86728600-86738800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:86728800-86737400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:86728800-86737800	Strong transcription	Duodenum Mucosa	Duodenum
40	chr2:86728800-86737800	Strong transcription	Placenta	Placenta
41	chr2:86729000-86734800	Weak transcription	Right Ventricle	heart
42	chr2:86729000-86736400	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr2:86729000-86737400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:86729000-86737800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr2:86729000-86738000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr2:86729000-86738000	Strong transcription	Thymus	Thymus
47	chr2:86729000-86738200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr2:86729000-86738400	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr2:86729000-86738600	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr2:86729000-86747000	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links