Variant report

Variant	rs12087441
Chromosome Location	chr1:174157834-174157835
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	chr1:174157753..174160187-chr1:174164644..174167517,2	MCF-7	breast:
2	chr1:174128241..174130281-chr1:174157762..174160299,2	K562	blood:

Variant related genes	Relation type
ENSG00000227373	Chromatin interaction
ENSG00000152061	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10158115	0.83[EUR][1000 genomes]
rs10158289	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10912734	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10912761	0.83[EUR][1000 genomes]
rs12079063	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12085290	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12094341	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12563301	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2064149	0.89[EUR][1000 genomes]
rs2143114	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2294492	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2860847	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2901785	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4650945	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4650989	0.84[EUR][1000 genomes]
rs4650990	0.83[EUR][1000 genomes]
rs4652234	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4652237	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4652294	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57366619	0.81[EUR][1000 genomes]
rs57919173	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60354115	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6425274	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6656188	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6658543	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6667267	0.89[EUR][1000 genomes]
rs6670617	0.87[EUR][1000 genomes]
rs6672986	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6681390	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6681618	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6681780	0.81[EUR][1000 genomes]
rs6690570	0.88[EUR][1000 genomes]
rs6695636	0.84[EUR][1000 genomes]
rs6696076	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7512930	0.83[EUR][1000 genomes]
rs7523460	0.83[EUR][1000 genomes]
rs7523938	0.82[EUR][1000 genomes]
rs7526024	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7533430	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7537517	0.90[EUR][1000 genomes]
rs7552830	0.83[EUR][1000 genomes]
rs7553788	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7555067	0.84[EUR][1000 genomes]
rs972361	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9787001	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv872552	chr1:174061844-174469748	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv1008314	chr1:174080192-174311023	Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
3	nsv535207	chr1:174080192-174311023	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
4	esv1799250	chr1:174119038-174484277	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv1800060	chr1:174132703-174501836	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv465672	chr1:174133251-174469905	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv548194	chr1:174133251-174469905	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv946458	chr1:174149182-174160829	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv470746	chr1:174150850-174469905	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174129600-174164800	Weak transcription	Gastric	stomach
2	chr1:174129600-174173200	Weak transcription	Pancreas	Pancrea
3	chr1:174134800-174159800	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:174136400-174160000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr1:174138400-174160000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:174139000-174159800	Weak transcription	Right Atrium	heart
7	chr1:174144000-174178200	Weak transcription	Left Ventricle	heart
8	chr1:174144200-174158000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr1:174148800-174159600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:174151800-174159600	Weak transcription	K562	blood
11	chr1:174154200-174173600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
12	chr1:174157600-174158000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
13	chr1:174157600-174158200	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr1:174157800-174158000	Weak transcription	Primary T cells from cord blood	blood
15	chr1:174157800-174158000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links