Variant report

Variant	rs11728254
Chromosome Location	chr4:149301579-149301580
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	chr4:149300581..149303429-chr4:149304550..149306545,2	MCF-7	breast:

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10012553	1.00[CHB][hapmap]
rs10519954	1.00[CHB][hapmap]
rs10519955	1.00[CHB][hapmap]
rs11725509	1.00[CHB][hapmap]
rs11726964	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11730006	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11937655	1.00[CHB][hapmap]
rs12506373	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12509783	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[YRI][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512334	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024506	1.00[CHB][hapmap]
rs17024631	1.00[CHB][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs17024633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs17024654	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024666	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024683	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024715	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2883917	1.00[CHB][hapmap]
rs34861534	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6829058	1.00[ASN][1000 genomes]
rs6831034	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6857339	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6858581	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs878152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027263	chr4:149127120-149320135	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv537296	chr4:149127120-149320135	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1016966	chr4:149209467-149341037	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv530433	chr4:149277637-149669181	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription 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	14 gene(s)	inside rSNPs	diseases
5	nsv880246	chr4:149287807-149311728	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv980434	chr4:149300843-149308003	Enhancers Weak transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:149277000-149306800	Weak transcription	Pancreas	Pancrea
2	chr4:149292200-149315000	Weak transcription	Fetal Muscle Leg	muscle
3	chr4:149297600-149304600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:149297800-149306000	Weak transcription	Rectal Smooth Muscle	rectum
5	chr4:149297800-149306000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr4:149297800-149306000	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:149297800-149350000	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr4:149298400-149311600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr4:149299000-149306000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr4:149299000-149306800	Weak transcription	Psoas Muscle	Psoas
11	chr4:149299000-149329000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:149299200-149306200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
13	chr4:149299200-149307000	Weak transcription	Ovary	ovary
14	chr4:149299200-149318400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr4:149299800-149307200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr4:149300600-149310000	Weak transcription	Left Ventricle	heart
17	chr4:149301200-149302000	Enhancers	Fetal Heart	heart
18	chr4:149301400-149301600	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr4:149301400-149301800	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr4:149301400-149302000	Enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links