Variant report

Variant	rs11265582
Chromosome Location	chr1:161255333-161255334
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161252880..161255836-chr1:161273696..161275808,2	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11265583	0.96[ASN][1000 genomes]
rs12023218	0.87[ASN][1000 genomes]
rs12025700	0.89[JPT][hapmap]
rs12049499	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12088460	1.00[ASN][1000 genomes]
rs12094828	0.90[ASN][1000 genomes]
rs12409590	0.91[ASN][1000 genomes]
rs12727003	0.83[ASN][1000 genomes]
rs16832745	0.89[JPT][hapmap]
rs2501862	0.89[JPT][hapmap]
rs2501867	0.88[ASN][1000 genomes]
rs2502813	0.89[ASN][1000 genomes]
rs34740003	0.83[ASN][1000 genomes]
rs4075971	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4255401	1.00[ASN][1000 genomes]
rs4271232	0.91[ASN][1000 genomes]
rs4436408	0.94[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4582821	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4636483	0.85[ASN][1000 genomes]
rs4636484	0.94[ASN][1000 genomes]
rs4657002	0.90[ASN][1000 genomes]
rs4657003	0.90[ASN][1000 genomes]
rs4657004	0.83[ASN][1000 genomes]
rs4657005	0.90[ASN][1000 genomes]
rs4657006	0.83[ASN][1000 genomes]
rs4657007	0.90[ASN][1000 genomes]
rs4657008	0.87[ASN][1000 genomes]
rs4657009	1.00[ASN][1000 genomes]
rs4657013	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs55748379	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61274438	0.81[ASN][1000 genomes]
rs6427581	0.94[ASW][hapmap];0.95[CEU][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6427583	0.90[ASN][1000 genomes]
rs6427584	1.00[ASN][1000 genomes]
rs6427588	0.85[CHB][hapmap];0.80[ASN][1000 genomes]
rs6657761	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6681182	0.82[ASN][1000 genomes]
rs6682220	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6690484	0.82[ASN][1000 genomes]
rs7532915	0.92[ASN][1000 genomes]
rs9427370	0.80[ASN][1000 genomes]
rs9651049	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9651050	0.85[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	nsv530077	chr1:160836448-161284904	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv432986	chr1:161221133-161673682	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11265582	FCRL4	cis	parietal	SCAN
rs11265582	PCP4L1	cis	parietal	SCAN
rs11265582	FCRL1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161238200-161257600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:161243000-161261200	Weak transcription	Brain Substantia Nigra	brain
3	chr1:161243200-161264000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr1:161244600-161256000	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:161250400-161274200	Weak transcription	Fetal Stomach	stomach
6	chr1:161252400-161274800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr1:161254000-161256600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
8	chr1:161254200-161255800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:161254400-161261200	Weak transcription	Brain Anterior Caudate	brain
10	chr1:161254800-161255800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:161254800-161255800	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr1:161254800-161255800	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr1:161255000-161255400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:161255000-161255600	Enhancers	H9 Cell Line	embryonic stem cell
15	chr1:161255000-161255800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:161255200-161255400	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr1:161255200-161255600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:161255200-161255600	Enhancers	Fetal Heart	heart
19	chr1:161255200-161255800	Enhancers	HUES64 Cell Line	embryonic stem cell
20	chr1:161255200-161256000	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr1:161255200-161274800	Weak transcription	Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links