Variant report

Variant	rs56333112
Chromosome Location	chr2:99059781-99059782
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	chr2:99059716..99061433-chr2:99224570..99226733,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115446	Chromatin interaction
ENSG00000183513	Chromatin interaction

Extended variants
information (count: 161 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:159)

rs_ID	r²[population]
rs10199199	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10496327	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10514774	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1139829	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11537554	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11884553	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11888595	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11896729	0.82[EUR][1000 genomes]
rs11901568	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11902825	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12052639	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12617721	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12618524	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619665	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12622341	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13402379	0.81[EUR][1000 genomes]
rs1516085	0.81[EUR][1000 genomes]
rs1587835	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17031139	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17031146	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17031905	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17032120	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17032866	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17032870	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17033136	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17033813	0.80[EUR][1000 genomes]
rs17034171	0.82[EUR][1000 genomes]
rs17034241	0.82[EUR][1000 genomes]
rs17444095	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17446058	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17502889	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17504774	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17505088	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17505326	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17506535	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17513468	0.81[EUR][1000 genomes]
rs1847550	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2230388	0.82[EUR][1000 genomes]
rs2276603	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2278206	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2278207	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2278208	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2278211	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2278212	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2278213	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2278214	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2309390	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3203856	0.82[EUR][1000 genomes]
rs34906456	0.82[EUR][1000 genomes]
rs3729568	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3754871	0.82[EUR][1000 genomes]
rs3754872	0.82[EUR][1000 genomes]
rs3754875	0.82[EUR][1000 genomes]
rs3754877	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3754878	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3754879	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3754880	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3754881	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3754883	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3754884	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3754885	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3754886	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3754888	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3754889	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3754890	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3754891	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3754892	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs3754893	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3769698	0.81[EUR][1000 genomes]
rs3769701	0.81[EUR][1000 genomes]
rs3769708	0.81[EUR][1000 genomes]
rs3769709	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3769712	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3769713	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3769715	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769716	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769717	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769719	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3769723	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3769724	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769725	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3769726	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769727	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3769728	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3769729	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3769730	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769733	0.80[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3769734	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769735	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3769736	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769737	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3769738	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3769740	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3769741	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3769743	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3820943	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3820945	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4596026	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4599165	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4850874	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4850875	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4850876	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4850877	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4850878	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4850879	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4851131	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851136	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851140	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4851141	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851142	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4851144	0.82[EUR][1000 genomes]
rs4851145	0.82[EUR][1000 genomes]
rs4851146	0.81[EUR][1000 genomes]
rs55900716	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55934321	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56091613	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56118505	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56141907	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56197140	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs56232707	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56240302	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56357378	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58778964	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61180742	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6542754	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6728891	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6736755	0.82[EUR][1000 genomes]
rs6753380	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6753515	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72819965	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72819970	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72819971	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72819972	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72819981	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72819996	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72820002	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72821904	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72821907	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72821908	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs72821920	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72821924	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72821930	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72821939	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72821943	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72821946	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72821951	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72821955	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs72821956	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72821965	0.81[EUR][1000 genomes]
rs72823788	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72823792	0.82[EUR][1000 genomes]
rs72823794	0.82[EUR][1000 genomes]
rs72823796	0.82[EUR][1000 genomes]
rs7562232	0.82[EUR][1000 genomes]
rs7585747	0.82[EUR][1000 genomes]
rs7585939	0.82[EUR][1000 genomes]
rs7588254	0.82[EUR][1000 genomes]
rs7593615	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs961242	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1006328	chr2:98977192-99210376	Strong transcription Weak transcription Enhancers Genic 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	8 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99057200-99060800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr2:99057400-99060800	Weak transcription	Fetal Heart	heart
3	chr2:99058000-99060600	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr2:99058200-99060800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr2:99058400-99060600	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr2:99058600-99059800	Enhancers	H1 Cell Line	embryonic stem cell
7	chr2:99058600-99059800	Enhancers	Fetal Intestine Large	intestine
8	chr2:99058600-99060600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr2:99058600-99060800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:99058800-99060600	Weak transcription	Primary monocytes fromperipheralblood	blood
11	chr2:99058800-99060600	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr2:99059000-99060400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr2:99059000-99060800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr2:99059000-99060800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr2:99059200-99060600	Weak transcription	Fetal Intestine Small	intestine
16	chr2:99059200-99060600	Weak transcription	HepG2	liver
17	chr2:99059200-99060800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr2:99059200-99060800	Weak transcription	Stomach Mucosa	stomach
19	chr2:99059400-99060400	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr2:99059400-99060400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:99059400-99060600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr2:99059400-99060600	Weak transcription	Duodenum Mucosa	Duodenum
23	chr2:99059400-99060600	Weak transcription	K562	blood
24	chr2:99059600-99060400	Enhancers	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links