Variant report

Variant	rs2607119
Chromosome Location	chr15:51992825-51992826
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr15:51992695-51992931	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:51990726..51993605-chr15:51996321..51998740,2	MCF-7	breast:
2	chr15:51984640..51986605-chr15:51992060..51993889,2	K562	blood:
3	chr15:51990868..51993765-chr15:52043379..52046034,2	K562	blood:
4	chr15:51984283..51986352-chr15:51990636..51992962,2	K562	blood:
5	chr15:51991390..51994698-chr15:51996190..51998071,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000259241	TF binding region
ENSG00000259377	Chromatin interaction
ENSG00000140280	Chromatin interaction
ENSG00000128872	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10519313	0.81[GIH][hapmap]
rs11070863	0.85[ASN][1000 genomes]
rs11631725	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11634955	0.88[ASN][1000 genomes]
rs11635216	0.81[GIH][hapmap]
rs11638106	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11638154	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1456299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1456300	0.95[ASN][1000 genomes]
rs2054166	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2168474	0.86[ASN][1000 genomes]
rs2278989	0.81[GIH][hapmap]
rs2278990	0.81[GIH][hapmap]
rs2305716	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2414105	0.81[GIH][hapmap]
rs2414106	0.81[GIH][hapmap]
rs2414109	0.81[GIH][hapmap]
rs2414111	0.82[GIH][hapmap]
rs2622775	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2652594	0.94[JPT][hapmap]
rs28576876	0.87[ASN][1000 genomes]
rs4775953	0.81[GIH][hapmap]
rs4775968	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs55982453	0.87[ASN][1000 genomes]
rs60060794	0.86[ASN][1000 genomes]
rs7167760	0.94[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap]
rs7168749	0.83[ASN][1000 genomes]
rs7170980	0.94[CHB][hapmap];0.91[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs7171884	0.94[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs7183479	0.94[CHB][hapmap]
rs744039	1.00[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8023455	0.94[CHB][hapmap];0.88[JPT][hapmap];0.86[ASN][1000 genomes]
rs8033234	0.94[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs8034197	0.85[ASN][1000 genomes]
rs8037167	0.81[GIH][hapmap]
rs8037340	0.85[ASN][1000 genomes]
rs8042840	0.81[GIH][hapmap]
rs9944241	0.81[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2607119	BCL2L10	cis	parietal	SCAN
rs2607119	DMXL2	cis	lymphoblastoid	seeQTL
rs2607119	TMOD2	cis	cerebellum	SCAN
rs2607119	DMXL2	Cis_1M	lymphoblastoid	RTeQTL
rs2607119	ARPP19	cis	parietal	SCAN
rs2607119	SCG3	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51974200-52018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:51974400-52005200	Weak transcription	Brain Anterior Caudate	brain
3	chr15:51974600-52016400	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr15:51975000-51993200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:51975200-51998400	Weak transcription	Brain Angular Gyrus	brain
6	chr15:51975600-52017200	Weak transcription	Fetal Brain Male	brain
7	chr15:51982200-51996600	Strong transcription	Fetal Brain Female	brain
8	chr15:51983000-52013200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr15:51983400-51998400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr15:51984800-52018600	Weak transcription	Brain Hippocampus Middle	brain
11	chr15:51986000-51998400	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:51989600-51993800	Strong transcription	Brain Germinal Matrix	brain
13	chr15:51990000-52016800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr15:51990200-51994200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr15:51990400-51997600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr15:51990600-51993600	Strong transcription	Brain Inferior Temporal Lobe	brain
17	chr15:51991000-51994200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr15:51991000-51994600	Weak transcription	K562	blood
19	chr15:51991400-52018800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr15:51992000-51993600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:51992200-52018800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:51992400-51994400	Strong transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:51992600-52008400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:51992800-51993200	Weak transcription	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links