Variant report

Variant	rs16835366
Chromosome Location	chr1:153468106-153468107
allele	A/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	chr1:153466147..153468573-chr1:153470167..153472287,2	MCF-7	breast:
2	chr1:153467594..153470337-chr1:153471683..153474675,2	K562	blood:
3	chr1:153323483..153340048-chr1:153448254..153469845,61	MCF-7	breast:
4	chr1:153467541..153469828-chr1:153502709..153505691,2	K562	blood:
5	chr1:153466848..153469559-chr1:153579592..153581140,2	K562	blood:
6	chr1:153359777..153361314-chr1:153466006..153468984,2	MCF-7	breast:
7	chr1:153366171..153367906-chr1:153465906..153468901,2	MCF-7	breast:
8	chr1:15850894..15851830-chr1:153468064..153468564,2	HCT-116	colon:
9	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
10	chr1:153438181..153439098-chr1:153467083..153468312,5	MCF-7	breast:
11	chr1:153324635..153326715-chr1:153466816..153468514,22	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000132906	Chromatin interaction
ENSG00000163220	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000163218	Chromatin interaction
ENSG00000263841	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs16835368	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16835382	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16835393	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs17695220	0.86[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1887039	0.86[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1964151	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2339696	0.85[ASN][1000 genomes]
rs28410699	0.85[ASN][1000 genomes]
rs28464843	0.85[ASN][1000 genomes]
rs28632016	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28635377	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28676601	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28707433	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879553	0.85[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3915524	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4272569	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs4430277	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs4845351	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs4845352	0.88[JPT][hapmap]
rs4845548	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845549	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845551	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845552	0.81[CEU][hapmap];0.86[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845553	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845554	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6587743	0.86[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6587745	0.85[ASN][1000 genomes]
rs6587746	0.85[ASN][1000 genomes]
rs6660055	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672390	1.00[CEU][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6679509	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684970	0.86[GIH][hapmap];0.90[JPT][hapmap]
rs6690638	0.82[ASN][1000 genomes]
rs6690712	0.82[ASN][1000 genomes]
rs6696893	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7515940	0.82[ASN][1000 genomes]
rs7518306	0.90[JPT][hapmap]
rs7520093	0.85[ASN][1000 genomes]
rs7534343	0.83[ASN][1000 genomes]
rs7534347	0.85[ASN][1000 genomes]
rs7534830	0.82[ASN][1000 genomes]
rs7537898	0.82[ASN][1000 genomes]
rs7544359	0.82[ASN][1000 genomes]
rs9436094	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9436095	0.80[EUR][1000 genomes];0.88[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	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
6	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16835366	PSMB4	cis	parietal	SCAN
rs16835366	PSMD4	cis	parietal	SCAN
rs16835366	LCE2C	cis	parietal	SCAN
rs16835366	GBA	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153462800-153479000	Weak transcription	Right Atrium	heart
2	chr1:153464000-153469600	Weak transcription	Fetal Lung	lung
3	chr1:153464400-153471400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:153465800-153468600	Enhancers	Fetal Heart	heart
5	chr1:153466200-153471200	Weak transcription	Aorta	Aorta
6	chr1:153466800-153468400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr1:153467000-153468400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:153467000-153468400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:153467200-153478000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:153467400-153468200	Enhancers	Primary B cells from cord blood	blood
11	chr1:153467400-153468200	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:153467400-153468400	Enhancers	Ovary	ovary
13	chr1:153467600-153468200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:153467600-153468200	Enhancers	Skeletal Muscle Female	skeletal muscle
15	chr1:153467600-153468400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr1:153467600-153468400	Enhancers	Fetal Muscle Leg	muscle
17	chr1:153467800-153468400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr1:153467800-153469200	Enhancers	H1 Cell Line	embryonic stem cell
19	chr1:153468000-153470800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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