Variant report

Variant	rs2122158
Chromosome Location	chr5:107561614-107561615
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	chr5:107560160..107562056-chr5:107581004..107583478,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10036343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10041907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10057905	0.87[YRI][hapmap]
rs10063449	0.92[EUR][1000 genomes]
rs10063866	0.86[CEU][hapmap];0.90[EUR][1000 genomes]
rs10071595	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10072270	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10075907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10455007	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs10463586	0.87[EUR][1000 genomes]
rs11743651	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs11744374	0.90[EUR][1000 genomes]
rs12515105	0.82[GIH][hapmap]
rs13178456	0.91[EUR][1000 genomes]
rs1849011	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2029104	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044709	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2044710	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs2167001	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2416188	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs28497144	0.88[EUR][1000 genomes]
rs286764	0.96[CEU][hapmap];0.91[EUR][1000 genomes]
rs286767	0.90[EUR][1000 genomes]
rs2922423	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2922424	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2922426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2922427	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2922428	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2922429	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2922430	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2922433	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2966795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2966797	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2966799	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2966811	0.86[AFR][1000 genomes]
rs34298471	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4541643	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4957550	0.84[GIH][hapmap]
rs4957553	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs4957554	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs4957751	1.00[CEU][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes]
rs4957753	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes]
rs55896795	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57222565	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6596770	0.88[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs6596771	0.90[EUR][1000 genomes]
rs6596777	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6870573	0.86[CHD][hapmap];0.82[GIH][hapmap]
rs6875297	1.00[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs6883082	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs7708996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7717747	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs7726298	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[EUR][1000 genomes]
rs9326725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs962680	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs989001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534281	chr5:107357579-107674981	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv830441	chr5:107450392-107614557	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv882683	chr5:107476501-107769095	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv882684	chr5:107521677-107695558	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv830442	chr5:107539150-107697020	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2122158	NCRNA00219	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:107516200-107584800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr5:107517000-107571800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr5:107546600-107590800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr5:107547000-107577200	Weak transcription	Fetal Intestine Large	intestine
5	chr5:107549200-107578000	Weak transcription	Pancreas	Pancrea
6	chr5:107551200-107569000	Weak transcription	Primary T cells from cord blood	blood
7	chr5:107551800-107567200	Weak transcription	Primary B cells from cord blood	blood
8	chr5:107551800-107568800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:107551800-107569600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr5:107552000-107578800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:107552000-107585000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:107553000-107575400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr5:107553000-107584800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr5:107553400-107590800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr5:107554600-107574200	Weak transcription	Primary B cells from peripheral blood	blood
16	chr5:107556200-107566000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr5:107556400-107580200	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr5:107557200-107568800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr5:107558000-107581000	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr5:107559400-107563800	Weak transcription	Ovary	ovary
21	chr5:107559800-107568800	Weak transcription	NHDF-Ad	bronchial
22	chr5:107560200-107568600	Weak transcription	Fetal Heart	heart
23	chr5:107561400-107595000	Weak transcription	Psoas Muscle	Psoas
24	chr5:107561600-107561800	Enhancers	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links