Variant report

Variant	rs9651049
Chromosome Location	chr1:161258972-161258973
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:161243431..161244989-chr1:161257310..161259716,2	MCF-7	breast:
2	chr1:161195976..161198786-chr1:161258890..161261359,3	K562	blood:

Variant related genes	Relation type
ENSG00000263548	Chromatin interaction
ENSG00000158882	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11265582	0.93[ASN][1000 genomes]
rs11265583	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12023218	0.92[ASN][1000 genomes]
rs12025700	0.89[JPT][hapmap]
rs12088460	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12094828	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12409590	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12727003	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16832745	0.89[JPT][hapmap]
rs2501862	0.89[JPT][hapmap]
rs2501867	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2501871	0.81[AMR][1000 genomes]
rs2501875	0.81[AMR][1000 genomes]
rs2502812	0.85[AMR][1000 genomes]
rs2502813	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34740003	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4075971	0.97[ASN][1000 genomes]
rs4255401	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4271232	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4436408	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4582821	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4636483	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4636484	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4657002	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4657003	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4657004	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs4657005	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4657006	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4657007	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4657008	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4657009	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4657013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4657016	0.80[CHB][hapmap];0.82[CHD][hapmap];0.82[ASN][1000 genomes]
rs61274438	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61802084	0.80[AMR][1000 genomes]
rs6427583	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6427584	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6427588	0.90[CHB][hapmap];0.85[CHD][hapmap];0.85[ASN][1000 genomes]
rs6681182	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6690484	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7532915	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs7545977	0.84[ASN][1000 genomes]
rs9427370	0.82[AMR][1000 genomes]
rs9651035	0.93[AFR][1000 genomes]
rs9651050	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9651049	OR6K3	cis	cerebellum	SCAN
rs9651049	OR10J3	cis	parietal	SCAN
rs9651049	FCRL1	cis	cerebellum	SCAN
rs9651049	LMNA	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:161243000-161261200	Weak transcription	Brain Substantia Nigra	brain
2	chr1:161243200-161264000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr1:161250400-161274200	Weak transcription	Fetal Stomach	stomach
4	chr1:161252400-161274800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr1:161254400-161261200	Weak transcription	Brain Anterior Caudate	brain
6	chr1:161255200-161274800	Weak transcription	Lung	lung
7	chr1:161255600-161260000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:161255600-161261200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr1:161255600-161274600	Weak transcription	Adipose Nuclei	Adipose
10	chr1:161255800-161259800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:161255800-161260800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:161255800-161261000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr1:161255800-161261200	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr1:161256400-161272800	Weak transcription	Primary T cells from cord blood	blood
15	chr1:161257600-161260400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:161258200-161259800	Weak transcription	HepG2	liver
17	chr1:161258200-161261000	Weak transcription	Fetal Intestine Large	intestine
18	chr1:161258200-161261000	Weak transcription	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links