Variant report

Variant	rs16862877
Chromosome Location	chr3:150562118-150562119
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:150454689..150455809-chr3:150561872..150563110,20	MCF-7	breast:
2	chr3:150482143..150484358-chr3:150560207..150562152,2	MCF-7	breast:
3	chr3:150440289..150441169-chr3:150562059..150562920,5	MCF-7	breast:
4	chr3:150454685..150455867-chr3:150561994..150563025,47	MCF-7	breast:
5	chr3:150478771..150485219-chr3:150560533..150565602,8	MCF-7	breast:
6	chr3:150491265..150491866-chr3:150562006..150562929,2	MCF-7	breast:
7	chr3:150473969..150474942-chr3:150562035..150562940,4	MCF-7	breast:
8	chr3:150559675..150563415-chr3:150563767..150567112,4	MCF-7	breast:
9	chr3:150440299..150441134-chr3:150562057..150563139,6	MCF-7	breast:
10	chr3:150486959..150487925-chr3:150562003..150562943,2	MCF-7	breast:
11	chr3:150454735..150455867-chr3:150561994..150563025,23	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000244265	Chromatin interaction
ENSG00000181788	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10513379	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs1220544	0.81[JPT][hapmap]
rs12629256	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1444198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1444199	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16862928	0.93[EUR][1000 genomes]
rs17283761	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2034158	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2037408	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2037409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679986	0.92[ASN][1000 genomes]
rs4680004	0.90[ASN][1000 genomes]
rs4680006	1.00[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs4680007	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs56285716	0.92[ASN][1000 genomes]
rs56659353	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58091102	0.82[ASN][1000 genomes]
rs58515064	0.80[EUR][1000 genomes]
rs60107900	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60336215	0.83[EUR][1000 genomes]
rs60979559	0.84[EUR][1000 genomes]
rs61132047	0.89[EUR][1000 genomes]
rs62282691	0.88[ASN][1000 genomes]
rs67193230	0.93[EUR][1000 genomes]
rs6768276	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs6775087	0.91[ASN][1000 genomes]
rs6781091	0.92[ASN][1000 genomes]
rs6783058	0.86[ASN][1000 genomes]
rs73152585	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	nsv818177	chr3:150541363-150566422	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16862877	TM4SF4	cis	cerebellum	SCAN
rs16862877	TM4SF4	cis	parietal	SCAN
rs16862877	FAM194A	cis	parietal	SCAN
rs16862877	UBQLN4	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150560600-150562200	Weak transcription	Ovary	ovary
2	chr3:150560600-150566400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:150560800-150563000	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr3:150560800-150563400	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr3:150561000-150563200	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr3:150561000-150563200	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr3:150561000-150563800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr3:150561200-150563000	Enhancers	Fetal Intestine Large	intestine
9	chr3:150561200-150563200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:150561200-150563200	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr3:150561400-150566000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:150561800-150562600	Enhancers	Placenta	Placenta

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