Variant report

Variant	rs2212969
Chromosome Location	chr4:106979479-106979480
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	chr4:106978527..106980178-chr4:106980635..106982411,2	MCF-7	breast:
2	chr4:106816125..106818142-chr4:106978874..106981523,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138785	Chromatin interaction
ENSG00000168743	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10004034	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10017707	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10155346	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10516530	0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10516531	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11097923	0.90[ASN][1000 genomes]
rs11936196	0.90[ASN][1000 genomes]
rs11938792	0.90[ASN][1000 genomes]
rs12508029	0.93[ASN][1000 genomes]
rs12512475	1.00[ASW][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17036581	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1988966	0.90[ASN][1000 genomes]
rs28600991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3113246	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34305991	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34909190	0.98[ASN][1000 genomes]
rs34923623	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4415033	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4441824	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4533833	0.98[ASN][1000 genomes]
rs4560491	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4582218	0.90[ASN][1000 genomes]
rs57983950	0.89[ASN][1000 genomes]
rs6533241	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6533244	0.89[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6836796	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6848855	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6853347	0.90[ASN][1000 genomes]
rs72960673	0.96[ASN][1000 genomes]
rs7442226	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7677394	0.94[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7680756	1.00[ASW][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7694217	0.90[ASN][1000 genomes]
rs9884121	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9991203	0.87[CHB][hapmap]
rs9993259	0.98[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	nsv1014993	chr4:106796019-106980727	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv522792	chr4:106895964-106982793	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:106959600-106983400	Weak transcription	HepG2	liver
2	chr4:106967600-106983600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr4:106967600-106983800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr4:106967800-106984200	Weak transcription	Primary hematopoietic stem cells	blood
5	chr4:106967800-106994600	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr4:106968000-106984600	Weak transcription	Primary B cells from cord blood	blood
7	chr4:106972400-106997000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:106973000-106982800	Weak transcription	Fetal Lung	lung
9	chr4:106977800-106980200	Enhancers	iPS-18 Cell Line	embryonic stem cell
10	chr4:106977800-106980200	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr4:106977800-106980400	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr4:106978000-106980400	Enhancers	iPS-15b Cell Line	embryonic stem cell
13	chr4:106978000-106980600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr4:106978200-106980600	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr4:106978800-106979800	Weak transcription	HUES6 Cell Line	embryonic stem cell
16	chr4:106979400-106979600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:106979400-106982800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr4:106979400-106983800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links