Variant report

Variant	rs17008611
Chromosome Location	chr2:73261850-73261851
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	chr2:73261709..73264635-chr2:73311097..73313338,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135631	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10166058	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10166220	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10167566	0.80[CEU][hapmap];0.86[JPT][hapmap]
rs10174548	0.81[JPT][hapmap]
rs10176939	0.94[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10177159	1.00[CEU][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes]
rs10178854	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10178944	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10180720	0.87[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs10180995	0.82[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs10189744	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10190861	0.80[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs10191665	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10192077	0.94[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10197305	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.96[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10209859	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1036512	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12233055	0.94[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes]
rs13385994	0.84[EUR][1000 genomes]
rs13388404	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13390072	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13393567	0.83[EUR][1000 genomes]
rs13400920	0.81[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs13400948	0.85[GIH][hapmap];0.80[MEX][hapmap]
rs13403757	0.81[JPT][hapmap]
rs13403781	0.81[JPT][hapmap]
rs13424057	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13427947	0.82[EUR][1000 genomes]
rs1370383	0.87[CEU][hapmap];0.97[GIH][hapmap];0.96[TSI][hapmap];0.96[EUR][1000 genomes]
rs1430349	0.82[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs17008571	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17008631	0.87[CEU][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs1864488	0.81[JPT][hapmap]
rs1992133	0.82[GIH][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs2421098	0.95[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs3813222	0.86[JPT][hapmap]
rs3901273	0.81[JPT][hapmap]
rs4144837	0.87[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4514897	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs4527230	0.96[EUR][1000 genomes]
rs55974516	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57536428	0.84[EUR][1000 genomes]
rs57937746	0.84[EUR][1000 genomes]
rs58993488	0.96[EUR][1000 genomes]
rs61161134	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61650913	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62147721	0.96[EUR][1000 genomes]
rs62147724	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62147732	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6546794	0.96[EUR][1000 genomes]
rs6546796	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6546797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6546800	0.81[JPT][hapmap]
rs6709938	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes]
rs6710362	0.93[ASN][1000 genomes]
rs6710739	0.87[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.83[EUR][1000 genomes]
rs6711891	1.00[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];0.96[TSI][hapmap]
rs6713655	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717553	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6719333	0.94[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6726940	1.00[CEU][hapmap];0.81[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6727269	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6727919	0.81[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs6729266	0.87[GIH][hapmap];0.81[JPT][hapmap]
rs6732369	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.96[TSI][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6736153	0.87[GIH][hapmap];0.81[JPT][hapmap]
rs6749237	0.86[JPT][hapmap]
rs6750069	0.94[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6754779	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6754858	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6757131	0.94[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6759243	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6759733	0.94[CEU][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes]
rs727470	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs732178	0.94[CEU][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs732179	0.94[CEU][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs732180	0.94[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7557173	0.82[GIH][hapmap];0.81[JPT][hapmap]
rs7559340	0.82[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.86[TSI][hapmap]
rs7566904	0.87[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs7570876	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7578757	0.93[EUR][1000 genomes]
rs7579770	1.00[CEU][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes]
rs7580216	0.94[CEU][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7597032	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7602651	0.82[GIH][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.89[TSI][hapmap]
rs891432	0.81[CEU][hapmap];0.81[JPT][hapmap]
rs891433	0.81[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs893258	0.86[JPT][hapmap]
rs893259	1.00[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs9309467	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002295	chr2:73216155-73350391	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17008611	SFXN5	cis	cerebellum	SCAN
rs17008611	RAB11FIP5	cis	multi-tissue	Pritchard
rs17008611	FIGLA	cis	parietal	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73207800-73263200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:73214200-73286400	Weak transcription	Psoas Muscle	Psoas
3	chr2:73215800-73263000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:73220600-73263200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:73221200-73263000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr2:73223200-73274600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:73233200-73270800	Weak transcription	Brain Germinal Matrix	brain
8	chr2:73236000-73264200	Weak transcription	Rectal Smooth Muscle	rectum
9	chr2:73246400-73263400	Weak transcription	K562	blood
10	chr2:73246400-73263600	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr2:73246400-73277400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr2:73246600-73283800	Weak transcription	Hela-S3	cervix
13	chr2:73247400-73283800	Weak transcription	Dnd41	blood
14	chr2:73248200-73277200	Weak transcription	HMEC	breast
15	chr2:73249000-73263600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:73249000-73270200	Weak transcription	Fetal Thymus	thymus
17	chr2:73249200-73265200	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:73249200-73276000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:73249400-73263000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:73249400-73265200	Weak transcription	Left Ventricle	heart
21	chr2:73249400-73267600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr2:73249400-73267600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:73249400-73284200	Weak transcription	Aorta	Aorta
24	chr2:73249400-73290000	Weak transcription	HUVEC	blood vessel
25	chr2:73249600-73263000	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr2:73249600-73263000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr2:73249600-73263200	Weak transcription	Esophagus	oesophagus
28	chr2:73249600-73263400	Weak transcription	Fetal Muscle Trunk	muscle
29	chr2:73249600-73263800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:73249600-73264000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:73249600-73264000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:73249600-73266400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr2:73249600-73267600	Weak transcription	Colon Smooth Muscle	Colon
34	chr2:73249600-73267600	Weak transcription	Lung	lung
35	chr2:73249600-73267800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr2:73249600-73271800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr2:73249600-73277000	Weak transcription	NH-A	brain
38	chr2:73249600-73290000	Weak transcription	NHLF	lung
39	chr2:73250000-73277200	Weak transcription	HSMMtube	muscle
40	chr2:73250200-73263200	Weak transcription	Stomach Smooth Muscle	stomach
41	chr2:73250200-73271400	Weak transcription	Thymus	Thymus
42	chr2:73250200-73284200	Weak transcription	Ovary	ovary
43	chr2:73250400-73263000	Weak transcription	Fetal Stomach	stomach
44	chr2:73250400-73265000	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:73250400-73267600	Weak transcription	Spleen	Spleen
46	chr2:73250400-73277200	Weak transcription	Placenta	Placenta
47	chr2:73250600-73263000	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr2:73250800-73271400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:73250800-73276800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:73251200-73263200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links