Variant report

Variant	rs2554340
Chromosome Location	chr15:52276713-52276714
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:52272788..52276993-chr15:52369760..52371998,4	MCF-7	breast:
2	chr15:52273590..52276860-chr15:52313793..52315606,3	MCF-7	breast:
3	chr15:52273618..52277217-chr15:52282042..52285418,5	MCF-7	breast:
4	chr15:52271637..52274025-chr15:52275587..52277212,2	MCF-7	breast:
5	chr15:52272035..52276768-chr15:52309954..52313442,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259438	Chromatin interaction
ENSG00000069956	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10152141	0.88[ASN][1000 genomes]
rs10518675	0.84[ASN][1000 genomes]
rs16964694	0.86[ASN][1000 genomes]
rs16964700	0.86[ASN][1000 genomes]
rs16964705	0.86[ASN][1000 genomes]
rs17612255	0.81[ASN][1000 genomes]
rs2001741	0.88[ASN][1000 genomes]
rs2017967	0.84[ASN][1000 genomes]
rs2246726	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2414120	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2414121	0.80[AMR][1000 genomes]
rs2414123	0.86[ASN][1000 genomes]
rs2441779	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2470593	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2470594	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2470595	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3099571	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4375608	0.93[ASN][1000 genomes]
rs4456445	0.93[ASN][1000 genomes]
rs4775993	0.84[ASN][1000 genomes]
rs4775995	0.84[ASN][1000 genomes]
rs55714716	0.90[ASN][1000 genomes]
rs55873482	0.88[ASN][1000 genomes]
rs56307802	0.84[ASN][1000 genomes]
rs56677715	0.88[ASN][1000 genomes]
rs58000475	0.86[ASN][1000 genomes]
rs61546369	0.88[ASN][1000 genomes]
rs7177328	0.88[ASN][1000 genomes]
rs7359204	0.98[ASN][1000 genomes]
rs74013636	0.93[ASN][1000 genomes]
rs74013638	0.88[ASN][1000 genomes]
rs74013640	0.88[ASN][1000 genomes]
rs74013641	0.88[ASN][1000 genomes]
rs74013642	0.88[ASN][1000 genomes]
rs74013644	0.84[ASN][1000 genomes]
rs74013645	0.84[ASN][1000 genomes]
rs74013646	0.84[ASN][1000 genomes]
rs74013647	0.84[ASN][1000 genomes]
rs74013648	0.84[ASN][1000 genomes]
rs74013653	0.86[ASN][1000 genomes]
rs74013654	0.84[ASN][1000 genomes]
rs74013656	0.81[ASN][1000 genomes]
rs74013657	0.81[ASN][1000 genomes]
rs751560	0.86[ASN][1000 genomes]
rs8033365	0.81[ASN][1000 genomes]
rs8033840	0.83[ASN][1000 genomes]
rs8040728	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs8041281	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs9796534	0.90[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	nsv1053788	chr15:52223389-52307138	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv1047260	chr15:52257100-52337418	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	nsv1050664	chr15:52265723-52342101	Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
4	nsv517399	chr15:52266878-52305464	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv569421	chr15:52268144-52282436	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
6	nsv1536	chr15:52276293-52320919	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52274600-52277200	Weak transcription	Fetal Intestine Small	intestine
2	chr15:52274600-52279200	Weak transcription	Right Atrium	heart
3	chr15:52274600-52284600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:52274800-52278800	Weak transcription	Brain Angular Gyrus	brain
5	chr15:52274800-52287200	Weak transcription	HSMMtube	muscle
6	chr15:52275800-52276800	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:52276200-52277000	Enhancers	HepG2	liver
8	chr15:52276400-52277000	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links