Variant report

Variant	rs5898
Chromosome Location	chr11:46749648-46749649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:46721940..46724006-chr11:46749499..46751031,2	MCF-7	breast:
2	chr11:46747479..46750421-chr11:46771928..46774649,2	MCF-7	breast:
3	chr11:46723694..46726091-chr11:46747520..46750064,2	K562	blood:
4	chr11:46744635..46748438-chr11:46749413..46751791,3	K562	blood:
5	chr11:46744635..46747178-chr11:46749413..46751721,2	K562	blood:

Variant related genes	Relation type
ENSG00000175216	Chromatin interaction
ENSG00000175220	Chromatin interaction
ENSG00000180210	Chromatin interaction
ENSG00000175213	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10466476	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10466477	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838634	1.00[ASN][1000 genomes]
rs11038985	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11038987	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039012	1.00[ASN][1000 genomes]
rs11039015	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs11822959	1.00[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11824327	0.88[CEU][hapmap];1.00[ASN][1000 genomes]
rs11825434	0.88[CEU][hapmap];1.00[ASN][1000 genomes]
rs12273360	1.00[ASN][1000 genomes]
rs12277006	0.88[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];1.00[ASN][1000 genomes]
rs12281784	1.00[ASN][1000 genomes]
rs12287376	1.00[ASN][1000 genomes]
rs12294921	1.00[ASN][1000 genomes]
rs16938534	0.88[CEU][hapmap];1.00[ASN][1000 genomes]
rs17787930	1.00[ASN][1000 genomes]
rs2867206	1.00[ASN][1000 genomes]
rs3136433	1.00[CEU][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]
rs3136434	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][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]
rs3136436	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136439	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][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]
rs3136443	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136446	1.00[CEU][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]
rs3136448	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136467	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136468	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136481	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136482	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136487	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3136489	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136496	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3136500	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][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]
rs3136504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3136521	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4128315	1.00[ASN][1000 genomes]
rs4500447	1.00[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56311746	1.00[ASN][1000 genomes]
rs56331152	1.00[ASN][1000 genomes]
rs57368576	1.00[ASN][1000 genomes]
rs57485117	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59197251	1.00[ASN][1000 genomes]
rs60940896	1.00[ASN][1000 genomes]
rs61382645	1.00[ASN][1000 genomes]
rs61882744	1.00[ASN][1000 genomes]
rs61882755	1.00[ASN][1000 genomes]
rs61884270	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884294	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884297	1.00[ASN][1000 genomes]
rs61884303	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884304	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884305	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884306	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884307	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897302	0.83[AFR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897303	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897304	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61897308	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61898529	1.00[ASN][1000 genomes]
rs61898531	1.00[ASN][1000 genomes]
rs61899280	1.00[ASN][1000 genomes]
rs61899282	1.00[ASN][1000 genomes]
rs61899283	1.00[ASN][1000 genomes]
rs6485700	0.88[CEU][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs6485706	1.00[ASN][1000 genomes]
rs7102325	1.00[ASN][1000 genomes]
rs7102474	1.00[ASN][1000 genomes]
rs7105052	1.00[CEU][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7105172	1.00[ASN][1000 genomes]
rs7105217	1.00[ASN][1000 genomes]
rs7106323	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7108147	1.00[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs7111760	1.00[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs7111811	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7112060	0.88[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs7112518	1.00[ASN][1000 genomes]
rs7115038	0.88[CEU][hapmap]
rs7115986	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7118097	1.00[ASN][1000 genomes]
rs7120113	1.00[ASN][1000 genomes]
rs7123729	1.00[ASN][1000 genomes]
rs7128102	1.00[ASN][1000 genomes]
rs7129622	1.00[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap];1.00[ASN][1000 genomes]
rs73456126	1.00[ASN][1000 genomes]
rs7928445	1.00[CEU][hapmap];0.91[GIH][hapmap];0.92[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7938960	1.00[ASN][1000 genomes]
rs7945548	1.00[ASN][1000 genomes]
rs7947517	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9667108	1.00[ASN][1000 genomes]
rs9735937	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044225	chr11:46472580-46771102	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv541030	chr11:46472580-46771102	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv430382	chr11:46743135-46849360	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46744400-46752000	Genic enhancers	Liver	Liver
2	chr11:46745000-46751200	Genic enhancers	HepG2	liver
3	chr11:46746000-46758000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr11:46746000-46762800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:46746200-46751000	Weak transcription	A549	lung
6	chr11:46746200-46761200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr11:46746200-46761400	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr11:46746400-46751000	Weak transcription	Esophagus	oesophagus
9	chr11:46748000-46750800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr11:46749400-46749800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr11:46749400-46750000	Active TSS	Spleen	Spleen
12	chr11:46749600-46749800	Enhancers	Aorta	Aorta
13	chr11:46749600-46750000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links