Variant report

Variant	rs16835368
Chromosome Location	chr1:153468701-153468702
allele	C/T
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	chr1:153467594..153470337-chr1:153471683..153474675,2	K562	blood:
2	chr1:153457718..153462195-chr1:153468437..153470953,3	K562	blood:
3	chr1:153459205..153462195-chr1:153468437..153470623,2	K562	blood:
4	chr1:153323483..153340048-chr1:153448254..153469845,61	MCF-7	breast:
5	chr1:153468303..153470815-chr1:153474677..153477799,3	K562	blood:
6	chr1:153467541..153469828-chr1:153502709..153505691,2	K562	blood:
7	chr1:153466848..153469559-chr1:153579592..153581140,2	K562	blood:
8	chr1:153359777..153361314-chr1:153466006..153468984,2	MCF-7	breast:
9	chr1:153366171..153367906-chr1:153465906..153468901,2	MCF-7	breast:
10	chr1:153320974..153341807-chr1:153456098..153486349,81	MCF-7	breast:
11	chr1:153360492..153363183-chr1:153468119..153469650,2	MCF-7	breast:

No data

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

Extended variants
information (count: 51 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs16835366	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];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16835393	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs17695220	0.85[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1887039	0.85[GIH][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1964151	0.97[AMR][1000 genomes];1.00[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	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28635377	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28676601	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28707433	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2879553	0.93[ASW][hapmap];0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs3915524	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4272569	0.85[GIH][hapmap];0.90[JPT][hapmap]
rs4430277	0.85[GIH][hapmap];0.90[JPT][hapmap]
rs4845351	0.85[GIH][hapmap];0.90[JPT][hapmap]
rs4845352	0.88[JPT][hapmap]
rs4845548	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845549	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845550	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845551	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4845552	0.81[CEU][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845553	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4845554	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs6587743	0.85[GIH][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs6587745	0.85[ASN][1000 genomes]
rs6587746	0.85[ASN][1000 genomes]
rs6660055	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672390	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6679509	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6684970	0.85[GIH][hapmap];0.90[JPT][hapmap]
rs6690638	0.82[ASN][1000 genomes]
rs6690712	0.82[ASN][1000 genomes]
rs6696893	0.90[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	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9436095	0.81[EUR][1000 genomes];0.88[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	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	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
4	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
5	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16835368	LCE2C	cis	parietal	SCAN
rs16835368	PSMD4	cis	parietal	SCAN
rs16835368	RN7SL44P	cis	Nerve Tibial	GTEx
rs16835368	PSMB4	cis	parietal	SCAN
rs16835368	GBA	cis	parietal	SCAN

Chromatin state (count:11 , 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	chr1:153466200-153471200	Weak transcription	Aorta	Aorta
5	chr1:153467200-153478000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:153467800-153469200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr1:153468000-153470800	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr1:153468400-153469400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:153468400-153471000	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:153468400-153471000	Weak transcription	Ovary	ovary
11	chr1:153468400-153479000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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