Variant report

Variant	rs16964476
Chromosome Location	chr15:51974224-51974225
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	chr15:51974117..51976857-chr15:51978812..51980643,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1010486	0.88[ASN][1000 genomes]
rs1017679	0.85[CHB][hapmap]
rs10519310	0.89[AMR][1000 genomes]
rs10519314	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10519315	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10519316	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10519318	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10519319	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10519320	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10519321	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1471072	0.85[CHB][hapmap]
rs16964465	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17648565	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs17648801	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17705035	1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2124588	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2124589	1.00[ASN][1000 genomes]
rs2124590	1.00[ASN][1000 genomes]
rs2305709	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2305711	1.00[ASN][1000 genomes]
rs2305712	0.87[ASN][1000 genomes]
rs2305715	1.00[ASN][1000 genomes]
rs2305719	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2622770	0.85[CHB][hapmap];0.90[JPT][hapmap];0.94[ASN][1000 genomes]
rs3214014	1.00[ASN][1000 genomes]
rs3764220	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3765067	0.98[ASN][1000 genomes]
rs3809498	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3816544	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs41286490	1.00[ASN][1000 genomes]
rs41286492	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs60337239	1.00[ASN][1000 genomes]
rs60437890	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs60934476	1.00[ASN][1000 genomes]
rs7163359	1.00[CHB][hapmap];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7174397	1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs74013290	0.89[AMR][1000 genomes]
rs8023804	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8032454	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv904219	chr15:51851999-51977159	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
3	nsv457139	chr15:51854718-51977159	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
4	nsv569407	chr15:51854718-51977159	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	n/a
5	nsv1035967	chr15:51949866-52008736	Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51973000-51974400	Active TSS	H9 Cell Line	embryonic stem cell
2	chr15:51973000-51974400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:51973000-51974600	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr15:51973000-51974600	Active TSS	HUES6 Cell Line	embryonic stem cell
5	chr15:51973000-51974800	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr15:51973000-51975000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
7	chr15:51973000-51975000	Active TSS	Fetal Brain Female	brain
8	chr15:51973000-51975400	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr15:51973200-51974400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr15:51973200-51974600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
11	chr15:51973200-51974600	Active TSS	H1 Cell Line	embryonic stem cell
12	chr15:51973200-51974600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:51973200-51974800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr15:51973200-51974800	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr15:51973200-51974800	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr15:51973400-51974400	Active TSS	Brain Anterior Caudate	brain
17	chr15:51973400-51974600	Active TSS	iPS-18 Cell Line	embryonic stem cell
18	chr15:51973400-51974600	Active TSS	Brain Cingulate Gyrus	brain
19	chr15:51973400-51975400	Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr15:51973600-51974400	Active TSS	Brain Hippocampus Middle	brain
21	chr15:51973600-51974600	Active TSS	Fetal Brain Male	brain
22	chr15:51973600-51974600	Active TSS	K562	blood
23	chr15:51973600-51975200	Active TSS	Brain Angular Gyrus	brain
24	chr15:51974000-51974400	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr15:51974000-51974400	Active TSS	Fetal Adrenal Gland	Adrenal Gland
26	chr15:51974000-51974600	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:51974000-51975200	Active TSS	Brain Germinal Matrix	brain
28	chr15:51974200-51974400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr15:51974200-51974400	Enhancers	Cortex derived primary cultured neurospheres	brain
30	chr15:51974200-51977200	Weak transcription	Brain Substantia Nigra	brain
31	chr15:51974200-52018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links