Variant report

Variant	rs10034172
Chromosome Location	chr4:106559599-106559600
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:106557959..106560192-chr4:106563157..106566031,2	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10023798	0.86[CEU][hapmap]
rs10025790	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10032142	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10032283	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516523	0.82[CEU][hapmap];0.94[CHD][hapmap]
rs11097895	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11722731	0.94[CHD][hapmap]
rs11726715	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11934139	0.82[CEU][hapmap];0.94[CHD][hapmap]
rs11941690	0.82[CEU][hapmap];0.94[CHD][hapmap]
rs13138544	0.93[CEU][hapmap];0.88[CHD][hapmap];0.88[MEX][hapmap];0.82[EUR][1000 genomes]
rs13147012	0.83[EUR][1000 genomes]
rs13148869	0.82[CEU][hapmap];0.94[CHD][hapmap]
rs1447093	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447094	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1447098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447099	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447100	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1447101	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036041	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17036098	0.93[CEU][hapmap]
rs17262764	0.82[CEU][hapmap];0.94[CHD][hapmap]
rs2044536	0.93[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2121558	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2544395	0.82[CEU][hapmap];0.94[CHD][hapmap]
rs2553449	0.83[CHB][hapmap];0.94[CHD][hapmap]
rs2553458	0.82[CEU][hapmap];0.94[CHD][hapmap]
rs2553468	0.82[CEU][hapmap];0.89[CHD][hapmap]
rs28415919	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796920	0.86[CEU][hapmap]
rs3822277	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4484305	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4699196	0.82[CEU][hapmap];0.94[CHD][hapmap]
rs6533214	0.82[MEX][hapmap]
rs6533218	0.82[CEU][hapmap];0.94[CHD][hapmap]
rs67822595	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6820200	0.81[CEU][hapmap]
rs6833345	0.86[CEU][hapmap]
rs7680134	0.84[EUR][1000 genomes]
rs7685231	0.94[CHD][hapmap]
rs7686722	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7699846	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs921113	0.88[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes]
rs9999133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9999326	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[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	nsv879699	chr4:106212562-106698892	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106545200-106577800	Weak transcription	Pancreas	Pancrea
2	chr4:106558400-106559600	Enhancers	iPS-20b Cell Line	embryonic stem cell
3	chr4:106558400-106559800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr4:106558600-106559800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:106559000-106559600	Enhancers	Brain Angular Gyrus	brain
6	chr4:106559200-106559800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr4:106559200-106559800	Enhancers	Cortex derived primary cultured neurospheres	brain
8	chr4:106559200-106560000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr4:106559200-106577800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr4:106559400-106559600	Enhancers	Brain Hippocampus Middle	brain
11	chr4:106559400-106560000	Enhancers	Fetal Lung	lung
12	chr4:106559400-106563000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr4:106559400-106563000	Weak transcription	Right Atrium	heart
14	chr4:106559400-106564200	Weak transcription	Small Intestine	intestine
15	chr4:106559400-106576600	Weak transcription	Fetal Intestine Large	intestine
16	chr4:106559400-106580000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:106559400-106580200	Weak transcription	Fetal Intestine Small	intestine
18	chr4:106559400-106602800	Weak transcription	Duodenum Mucosa	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links