Variant report

Variant	rs10084984
Chromosome Location	chr4:95254575-95254576
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95253673..95254779-chr4:95311169..95313000,5	MCF-7	breast:
2	chr4:95248894..95251809-chr4:95252736..95255390,4	K562	blood:
3	chr4:95254114..95254772-chr4:95516666..95517241,2	MCF-7	breast:
4	chr4:95254030..95254909-chr4:95311486..95312552,3	K562	blood:

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10003038	1.00[CEU][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10007463	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10014718	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10016925	0.93[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10018599	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10022350	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10022504	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs10025333	1.00[CEU][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs10025839	0.83[EUR][1000 genomes]
rs10027578	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10029551	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10030605	1.00[CEU][hapmap];1.00[GIH][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs10032125	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs10516948	0.87[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];0.89[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11947499	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12186176	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs17303283	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs17310498	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17374902	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17374964	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17376684	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17378658	0.83[GIH][hapmap]
rs28379069	0.81[EUR][1000 genomes]
rs28419190	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs28442028	0.81[EUR][1000 genomes]
rs28469826	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs28470897	0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs28508438	0.84[AMR][1000 genomes]
rs28521014	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28544271	0.81[EUR][1000 genomes]
rs28568937	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28581732	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28593606	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28638427	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs28650373	0.95[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28711614	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28713352	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28795707	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs41275681	0.87[EUR][1000 genomes]
rs6811367	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6817118	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6834248	0.82[CEU][hapmap];0.89[TSI][hapmap]
rs6844517	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6848140	0.82[AFR][1000 genomes]
rs6848742	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.94[MKK][hapmap];0.96[TSI][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs6857003	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs728989	0.82[CEU][hapmap]
rs7653910	0.87[EUR][1000 genomes]
rs7654621	1.00[CEU][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7660243	0.81[EUR][1000 genomes]
rs7661682	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs7685653	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9307138	1.00[CEU][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9307140	0.93[CEU][hapmap]
rs9884428	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9991214	1.00[CEU][hapmap];0.89[YRI][hapmap];0.82[EUR][1000 genomes]
rs9992255	1.00[CEU][hapmap];0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9999328	0.82[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9999656	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10084984	AIRE	trans	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95248800-95255000	Weak transcription	Adipose Nuclei	Adipose
2	chr4:95249000-95260800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:95249400-95261000	Weak transcription	Placenta	Placenta
4	chr4:95252800-95254800	Enhancers	Fetal Intestine Small	intestine
5	chr4:95252800-95257200	Weak transcription	Gastric	stomach
6	chr4:95254000-95254800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr4:95254000-95255200	Enhancers	Fetal Heart	heart
8	chr4:95254000-95255600	Enhancers	HUES6 Cell Line	embryonic stem cell
9	chr4:95254000-95259200	Weak transcription	Primary hematopoietic stem cells	blood
10	chr4:95254200-95254800	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr4:95254200-95254800	Enhancers	Fetal Intestine Large	intestine
12	chr4:95254400-95254600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr4:95254400-95254600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr4:95254400-95254600	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr4:95254400-95254600	Enhancers	K562	blood
16	chr4:95254400-95254800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr4:95254400-95254800	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr4:95254400-95254800	Enhancers	A549	lung
19	chr4:95254400-95255000	Enhancers	iPS-18 Cell Line	embryonic stem cell
20	chr4:95254400-95255000	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr4:95254400-95255200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr4:95254400-95255200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr4:95254400-95255400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:95254400-95259800	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links