Variant report

Variant	rs4550716
Chromosome Location	chr2:47717907-47717908
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:47717663-47717926	K562	blood:	n/a	n/a
2	POLR2A	chr2:47717819-47717938	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr2:47717810-47717978	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
ENSG00000236558	TF binding region

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10175959	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10188090	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10197011	0.80[AMR][1000 genomes]
rs10209369	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495945	0.82[CHB][hapmap]
rs11684661	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11684737	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11694689	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11886591	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[JPT][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12712993	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12712994	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1981927	0.88[EUR][1000 genomes]
rs2059520	0.81[CHB][hapmap];0.81[JPT][hapmap];0.85[ASN][1000 genomes]
rs2162121	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2347794	0.83[EUR][1000 genomes]
rs2347795	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3732182	0.80[ASN][1000 genomes]
rs3732183	0.80[ASN][1000 genomes]
rs3764960	0.81[ASN][1000 genomes]
rs3771274	0.96[CEU][hapmap];0.84[CHB][hapmap];0.81[JPT][hapmap];0.92[YRI][hapmap];0.88[EUR][1000 genomes]
rs3771275	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3771276	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3771280	0.82[CEU][hapmap];0.89[CHB][hapmap]
rs3771281	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3821227	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4452202	0.82[EUR][1000 genomes]
rs4583514	0.96[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[YRI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4596025	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6544989	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6544990	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6544992	0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6704794	0.85[EUR][1000 genomes]
rs6707467	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6711675	0.86[CEU][hapmap];0.85[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6718364	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6719539	0.88[EUR][1000 genomes]
rs6720549	0.94[ASN][1000 genomes]
rs6720555	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6724382	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6724876	0.86[AMR][1000 genomes]
rs6726832	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6729015	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6739590	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6754473	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6758327	0.87[AMR][1000 genomes]
rs6759990	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7565513	0.81[ASN][1000 genomes]
rs7575871	0.83[EUR][1000 genomes]
rs7586575	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7596629	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7599880	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7601062	0.86[AMR][1000 genomes]
rs7607312	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs876936	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs876937	0.80[EUR][1000 genomes]
rs9784092	0.84[AMR][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	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv999576	chr2:47506116-47773960	Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 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	chr2:47658200-47724800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:47702800-47727000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:47703800-47722000	Weak transcription	Brain Hippocampus Middle	brain
4	chr2:47712800-47721800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:47713600-47718200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr2:47714600-47727200	Weak transcription	Primary T cells from cord blood	blood
7	chr2:47715000-47721800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr2:47715400-47718000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:47715600-47718000	Enhancers	NHEK	skin
10	chr2:47715600-47718200	Enhancers	HMEC	breast
11	chr2:47715800-47718000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr2:47716600-47719200	Weak transcription	HUVEC	blood vessel
13	chr2:47716600-47720400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:47717000-47726200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr2:47717800-47718000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin

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