Variant report

Variant	rs3754892
Chromosome Location	chr2:99063318-99063319
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99062866..99063818-chr2:99134237..99134814,3	MCF-7	breast:
2	chr2:99059903..99063646-chr2:99224086..99226361,3	MCF-7	breast:
3	chr2:99061518..99063442-chr2:99098258..99101170,2	MCF-7	breast:
4	chr2:99063252..99065691-chr2:99066055..99068717,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183513	Chromatin interaction
ENSG00000115446	Chromatin interaction

Extended variants
information (count: 126 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:124)

rs_ID	r²[population]
rs10199199	0.86[ASN][1000 genomes]
rs10496327	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10514774	0.95[ASN][1000 genomes]
rs11537554	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs11884553	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11888595	0.97[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11892744	0.92[CHB][hapmap]
rs11896729	1.00[CHB][hapmap];0.81[JPT][hapmap]
rs11901568	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11902825	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12052639	0.92[ASN][1000 genomes]
rs12617721	0.82[ASN][1000 genomes]
rs12618524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12622341	0.97[ASN][1000 genomes]
rs13402379	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs1516085	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs1587835	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17031139	0.86[ASN][1000 genomes]
rs17031146	0.97[ASN][1000 genomes]
rs17031905	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs17032120	0.82[ASN][1000 genomes]
rs17032866	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17032870	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17033813	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17034171	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs17444095	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17446058	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs17502889	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17504774	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17505088	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs17505326	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17506535	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs1847550	0.86[ASN][1000 genomes]
rs2276603	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2278207	0.82[ASN][1000 genomes]
rs2278208	0.85[ASN][1000 genomes]
rs2278211	0.91[ASN][1000 genomes]
rs2278212	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2278213	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs2278214	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3203856	0.92[CHB][hapmap];0.87[JPT][hapmap]
rs3729568	1.00[CHB][hapmap];0.93[JPT][hapmap];0.80[ASN][1000 genomes]
rs3754872	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3754875	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3754877	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3754878	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3754879	0.81[ASN][1000 genomes]
rs3754880	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3754881	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3754884	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3754885	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3754886	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3754888	0.82[ASN][1000 genomes]
rs3754889	0.97[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3754890	0.97[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3754891	1.00[CHB][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs3754893	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3769698	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs3769701	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs3769708	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs3769712	0.85[ASN][1000 genomes]
rs3769715	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3769716	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3769717	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3769719	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3769724	0.89[ASN][1000 genomes]
rs3769726	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3769727	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3769728	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs3769729	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs3769730	0.91[ASN][1000 genomes]
rs3769733	0.83[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs3769734	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs3769735	0.82[ASN][1000 genomes]
rs3769736	0.94[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3769737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3769738	0.85[ASN][1000 genomes]
rs3769740	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs3769741	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs3769743	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs3820943	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs3820945	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4599165	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4850874	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs4850875	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4850876	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4850877	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4850878	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4850879	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4851131	0.97[ASN][1000 genomes]
rs4851136	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs4851138	1.00[CHB][hapmap];0.93[JPT][hapmap]
rs4851140	0.97[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4851141	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs4851142	1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AFR][1000 genomes]
rs4851145	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs4851146	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs55900716	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs55934321	0.91[ASN][1000 genomes]
rs56091613	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs56118505	0.89[ASN][1000 genomes]
rs56141907	0.82[AFR][1000 genomes]
rs56232707	0.97[ASN][1000 genomes]
rs56240302	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs56333112	0.91[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs56357378	0.97[ASN][1000 genomes]
rs61180742	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6542754	0.83[ASN][1000 genomes]
rs6728891	0.97[ASN][1000 genomes]
rs6736755	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs72819965	0.93[ASN][1000 genomes]
rs72819970	0.97[ASN][1000 genomes]
rs72819971	0.97[ASN][1000 genomes]
rs72819972	0.97[ASN][1000 genomes]
rs72819981	0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs72819996	0.97[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs72820002	0.86[ASN][1000 genomes]
rs72821904	0.97[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs72821907	0.88[ASN][1000 genomes]
rs72821908	0.82[ASN][1000 genomes]
rs72821920	0.91[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs72821939	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7588254	1.00[CHB][hapmap];0.87[JPT][hapmap]
rs7593615	0.86[ASN][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:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99060800-99063800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:99061200-99063400	Active TSS	Primary T cells fromperipheralblood	blood
3	chr2:99061800-99063400	Flanking Active TSS	Primary B cells from cord blood	blood
4	chr2:99061800-99064000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
5	chr2:99062000-99063600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr2:99062000-99063600	Enhancers	Spleen	Spleen
7	chr2:99062000-99063800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
8	chr2:99062000-99064000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr2:99062000-99064400	Flanking Active TSS	Dnd41	blood
10	chr2:99062200-99063600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:99062200-99063600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr2:99062200-99063600	Flanking Active TSS	Fetal Brain Female	brain
13	chr2:99062200-99063800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
14	chr2:99062200-99063800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr2:99062200-99063800	Flanking Active TSS	Thymus	Thymus
16	chr2:99062400-99063400	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr2:99062400-99063800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
18	chr2:99062400-99068400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr2:99062600-99063600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:99062600-99063600	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:99062600-99063600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr2:99062600-99063600	Enhancers	Fetal Muscle Trunk	muscle
23	chr2:99062600-99063600	Enhancers	Fetal Muscle Leg	muscle
24	chr2:99062600-99063600	Enhancers	Lung	lung
25	chr2:99062600-99063600	Enhancers	Sigmoid Colon	Sigmoid Colon
26	chr2:99062600-99063800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:99062600-99063800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
28	chr2:99062600-99063800	Active TSS	Brain Cingulate Gyrus	brain
29	chr2:99062600-99064000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr2:99062600-99064400	Flanking Active TSS	Primary T cells from cord blood	blood
31	chr2:99062600-99068600	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr2:99062800-99063600	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr2:99062800-99063600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr2:99062800-99063600	Active TSS	Duodenum Mucosa	Duodenum
35	chr2:99062800-99063600	Enhancers	Fetal Intestine Large	intestine
36	chr2:99062800-99063600	Enhancers	Fetal Lung	lung
37	chr2:99062800-99063600	Enhancers	Left Ventricle	heart
38	chr2:99062800-99063600	Active TSS	Rectal Mucosa Donor 29	rectum
39	chr2:99062800-99063600	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr2:99062800-99063600	Enhancers	A549	lung
41	chr2:99062800-99063600	Enhancers	NHEK	skin
42	chr2:99062800-99063800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr2:99062800-99063800	Enhancers	Primary monocytes fromperipheralblood	blood
44	chr2:99062800-99063800	Flanking Active TSS	GM12878-XiMat	blood
45	chr2:99062800-99063800	Enhancers	NHDF-Ad	bronchial
46	chr2:99062800-99064000	Enhancers	Primary hematopoietic stem cells	blood
47	chr2:99062800-99064400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr2:99062800-99066200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:99062800-99066600	Weak transcription	HMEC	breast
50	chr2:99062800-99070600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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