Variant report

Variant	rs2329999
Chromosome Location	chr5:42849236-42849237
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	chr5:42849114..42851312-chr5:42872827..42874820,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10038285	0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs10038477	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10041130	0.89[JPT][hapmap]
rs10044169	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10061833	0.92[CHB][hapmap];0.80[CHD][hapmap];0.89[JPT][hapmap]
rs10074740	0.91[CHB][hapmap];0.88[JPT][hapmap]
rs10077296	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs10941583	0.89[JPT][hapmap]
rs10941590	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs11745003	0.89[EUR][1000 genomes]
rs12652476	0.89[JPT][hapmap]
rs12654861	0.89[JPT][hapmap]
rs13153760	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13153784	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs13154178	0.96[CEU][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13184699	0.89[EUR][1000 genomes]
rs1364025	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1423655	0.89[JPT][hapmap]
rs16872680	0.88[JPT][hapmap]
rs16872694	0.89[JPT][hapmap]
rs16872762	0.89[JPT][hapmap]
rs16872777	0.89[JPT][hapmap]
rs16872791	0.89[JPT][hapmap]
rs16872830	0.81[ASN][1000 genomes]
rs16872832	0.81[ASN][1000 genomes]
rs17299359	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17299387	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1895456	0.98[EUR][1000 genomes]
rs28919903	0.88[JPT][hapmap]
rs2910860	0.89[JPT][hapmap]
rs2910878	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2910879	0.89[JPT][hapmap]
rs2972780	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs2972991	0.89[JPT][hapmap]
rs2973004	0.88[JPT][hapmap]
rs35566985	0.89[EUR][1000 genomes]
rs4146624	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4242117	0.81[JPT][hapmap]
rs4242119	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs4273617	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs4547964	0.82[JPT][hapmap]
rs4637559	0.86[JPT][hapmap]
rs4866948	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs6179	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs6182	0.89[JPT][hapmap]
rs6184	0.89[JPT][hapmap]
rs7703289	0.95[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7709215	0.91[EUR][1000 genomes]
rs7721598	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv597886	chr5:42610409-42854408	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
5	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
6	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
7	nsv523033	chr5:42752037-42919685	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv965602	chr5:42767568-42889585	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
10	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
11	nsv534185	chr5:42804840-43067088	Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	165 gene(s)	inside rSNPs	diseases
12	nsv1018276	chr5:42809131-42975245	Strong transcription Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2329999	RPL37	cis	cerebellum	SCAN
rs2329999	CARD6	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42844400-42851400	Weak transcription	Fetal Intestine Small	intestine
2	chr5:42847800-42851800	Weak transcription	K562	blood
3	chr5:42848200-42849400	Enhancers	HepG2	liver

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