Variant report

Variant	rs9812620
Chromosome Location	chr3:24469470-24469471
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:24469189..24471394-chr3:24471942..24474677,2	MCF-7	breast:
2	chr3:24468236..24470547-chr3:24471524..24477489,5	K562	blood:
3	chr3:24468904..24470956-chr3:24474502..24476814,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000229756	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1010163	0.93[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070456	1.00[JPT][hapmap];0.82[TSI][hapmap]
rs13070554	1.00[JPT][hapmap]
rs13077437	1.00[JPT][hapmap]
rs13086758	1.00[JPT][hapmap]
rs13098564	0.81[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17787379	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs2196432	0.93[CEU][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34832185	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34833017	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35493522	0.87[EUR][1000 genomes]
rs35892303	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36186467	0.86[EUR][1000 genomes]
rs3943744	0.93[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4557108	0.86[EUR][1000 genomes]
rs4858117	1.00[JPT][hapmap]
rs71328479	0.84[EUR][1000 genomes]
rs734866	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7626512	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817628	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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	nsv834640	chr3:24339779-24493605	Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv834641	chr3:24465862-24633738	Enhancers Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:24442000-24469800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr3:24443800-24475800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:24446000-24476800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr3:24458400-24469800	Weak transcription	Right Ventricle	heart
5	chr3:24458800-24490200	Weak transcription	Colon Smooth Muscle	Colon
6	chr3:24460800-24476600	Weak transcription	Left Ventricle	heart
7	chr3:24464600-24469800	Weak transcription	Psoas Muscle	Psoas
8	chr3:24464800-24475400	Weak transcription	Aorta	Aorta
9	chr3:24466200-24474600	Weak transcription	Fetal Intestine Small	intestine
10	chr3:24467200-24470000	Enhancers	Brain Germinal Matrix	brain
11	chr3:24468400-24469600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:24468400-24470200	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr3:24468400-24470600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr3:24468400-24470600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr3:24468600-24469800	Weak transcription	Fetal Brain Female	brain
16	chr3:24468600-24470000	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr3:24468600-24470200	Enhancers	Primary hematopoietic stem cells	blood
18	chr3:24468800-24469800	Weak transcription	Brain Substantia Nigra	brain
19	chr3:24469000-24469800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:24469000-24471400	Weak transcription	Fetal Lung	lung
21	chr3:24469000-24471800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:24469200-24470000	Weak transcription	Fetal Brain Male	brain

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