Variant report

Variant	rs575871
Chromosome Location	chr11:71778822-71778823
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:71778482..71780847-chr11:71823918..71825568,2	MCF-7	breast:
2	chr11:71777361..71780119-chr11:71790891..71793278,3	MCF-7	breast:
3	chr11:71743810..71760160-chr11:71777190..71805714,79	MCF-7	breast:
4	chr11:71749103..71754368-chr11:71778297..71785639,14	MCF-7	breast:
5	chr11:71761716..71763400-chr11:71778693..71780615,2	MCF-7	breast:
6	chr11:71776798..71779888-chr11:71780509..71784751,5	K562	blood:
7	chr11:71777400..71779303-chr11:72480443..72481955,2	MCF-7	breast:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LAMTOR1-3	chr11:71776245-71779277	NONHSAT022749

No data

Variant related genes	Relation type
ENSG00000137497	Chromatin interaction
ENSG00000263742	Chromatin interaction
ENSG00000206783	Chromatin interaction
ENSG00000184154	Chromatin interaction

Extended variants
information (count: 145 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:143)

rs_ID	r²[population]
rs10128658	0.87[CEU][hapmap]
rs10450664	0.87[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];0.84[JPT][hapmap]
rs10501408	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1055452	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs1057992	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10736783	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs10751189	0.87[CEU][hapmap]
rs10751191	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10793011	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs10793016	0.87[CEU][hapmap]
rs11235440	0.87[CEU][hapmap]
rs11235441	1.00[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11235444	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12272086	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12272213	0.87[CEU][hapmap];0.84[JPT][hapmap]
rs12275171	1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[JPT][hapmap];0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs12293195	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs12293885	0.87[CEU][hapmap]
rs12417471	0.87[AMR][1000 genomes]
rs1541304	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1541306	0.87[CEU][hapmap]
rs1548348	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1573501	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1573502	0.87[CEU][hapmap]
rs17161966	0.87[CEU][hapmap]
rs17161980	0.87[CEU][hapmap]
rs1892920	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1892921	0.87[CEU][hapmap]
rs1894004	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1939242	0.87[CEU][hapmap]
rs1939243	0.87[CEU][hapmap]
rs1939247	0.87[CEU][hapmap]
rs2155142	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs2155145	0.87[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2187496	0.86[CEU][hapmap];0.92[JPT][hapmap]
rs2250866	0.87[CEU][hapmap]
rs2276384	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs2276396	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2298456	0.87[CEU][hapmap]
rs2298457	0.87[CEU][hapmap]
rs2503	1.00[CEU][hapmap];0.93[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2508856	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2508860	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2511079	0.87[CEU][hapmap]
rs2511114	0.87[CEU][hapmap]
rs2511120	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2735787	0.80[ASN][1000 genomes]
rs2885880	0.83[JPT][hapmap]
rs3018301	0.87[CEU][hapmap]
rs3018302	0.87[CEU][hapmap]
rs3018310	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3750907	0.89[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs3750908	0.87[CEU][hapmap]
rs3793938	0.87[CEU][hapmap]
rs3814721	0.87[CEU][hapmap]
rs3829215	0.85[CHB][hapmap]
rs4121395	0.87[CEU][hapmap]
rs4245463	0.80[ASN][1000 genomes]
rs4338555	0.87[CEU][hapmap]
rs4378421	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4387373	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4412771	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4477459	0.87[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs482197	0.91[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs493065	0.87[CEU][hapmap]
rs4943821	0.87[CEU][hapmap]
rs4944232	0.87[CEU][hapmap]
rs4944242	0.87[CEU][hapmap]
rs4944243	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4945378	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4945392	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs4945426	0.87[CEU][hapmap]
rs4945434	0.87[CEU][hapmap]
rs510925	1.00[CEU][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes]
rs541022	0.87[CEU][hapmap];0.83[GIH][hapmap]
rs541228	0.82[AMR][1000 genomes]
rs542097	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap]
rs552966	0.87[CEU][hapmap]
rs560777	0.87[CEU][hapmap]
rs564294	0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs567026	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs575831	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs577435	1.00[CEU][hapmap];0.93[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs579320	0.86[CEU][hapmap]
rs58417942	0.80[ASN][1000 genomes]
rs585228	0.86[CEU][hapmap]
rs595062	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs60054591	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs607446	0.87[CEU][hapmap]
rs610004	0.87[CEU][hapmap]
rs610041	0.87[CEU][hapmap]
rs612255	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs628025	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs642573	0.87[CEU][hapmap]
rs642618	0.87[CEU][hapmap]
rs645603	0.91[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6592447	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs6592448	0.87[CEU][hapmap]
rs6592449	0.87[CEU][hapmap]
rs6592450	0.87[CEU][hapmap]
rs6592451	1.00[CEU][hapmap]
rs6592453	0.87[CEU][hapmap]
rs6592455	0.87[CEU][hapmap]
rs6592456	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6592457	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs659513	0.87[CEU][hapmap]
rs661290	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs671132	0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs671681	0.87[CEU][hapmap]
rs673478	0.87[CEU][hapmap]
rs674319	0.93[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs679926	0.87[CEU][hapmap]
rs686340	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7101553	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs7102192	0.87[CEU][hapmap]
rs7103210	0.86[CEU][hapmap]
rs7106730	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs7111379	1.00[CEU][hapmap];0.93[CHB][hapmap];0.92[JPT][hapmap];0.91[AMR][1000 genomes]
rs7113436	1.00[CEU][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs7113549	0.87[CEU][hapmap]
rs7115513	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7121080	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7121260	0.87[CEU][hapmap]
rs7123992	0.82[CEU][hapmap]
rs7126394	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7127865	0.87[CEU][hapmap]
rs7128317	0.87[CEU][hapmap]
rs7128974	0.87[CEU][hapmap]
rs73543612	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs73543635	0.91[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs73543640	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs73543643	0.91[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7924834	1.00[CEU][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap]
rs7925411	0.85[CEU][hapmap];0.84[CHB][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap]
rs7925604	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap]
rs7930544	0.86[CEU][hapmap]
rs7931941	0.87[CEU][hapmap]
rs7937515	0.85[JPT][hapmap]
rs7948821	0.87[CEU][hapmap]
rs947932	0.87[CEU][hapmap]
rs949323	0.90[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[ASN][1000 genomes]
rs949326	0.90[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs9666346	0.89[AMR][1000 genomes];0.85[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	nsv530623	chr11:71088949-72020418	Enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv428262	chr11:71363639-71804055	Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs575871	NUMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71754200-71780200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr11:71754200-71780400	Weak transcription	Aorta	Aorta
3	chr11:71754200-71789600	Weak transcription	Fetal Brain Female	brain
4	chr11:71754800-71781000	Weak transcription	Fetal Intestine Large	intestine
5	chr11:71755000-71780800	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr11:71755200-71780400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr11:71755400-71783000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr11:71756200-71783200	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr11:71757000-71783200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr11:71760000-71780400	Weak transcription	Left Ventricle	heart
11	chr11:71760400-71780200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr11:71760400-71780400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr11:71760400-71780400	Weak transcription	Liver	Liver
14	chr11:71760400-71780400	Weak transcription	Ovary	ovary
15	chr11:71760400-71780600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr11:71760600-71780400	Weak transcription	Gastric	stomach
17	chr11:71760600-71780800	Weak transcription	Spleen	Spleen
18	chr11:71767400-71786400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr11:71768000-71780200	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr11:71768000-71780400	Weak transcription	Small Intestine	intestine
21	chr11:71769200-71780400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:71769600-71780000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr11:71770000-71780400	Weak transcription	Right Ventricle	heart
24	chr11:71770000-71783200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr11:71770400-71780200	Weak transcription	HSMMtube	muscle
26	chr11:71770600-71781000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr11:71771400-71780600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
28	chr11:71771600-71779200	Weak transcription	Esophagus	oesophagus
29	chr11:71771600-71780000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr11:71771600-71789800	Weak transcription	Fetal Brain Male	brain
31	chr11:71773200-71779000	Weak transcription	Thymus	Thymus
32	chr11:71773200-71779200	Weak transcription	Lung	lung
33	chr11:71773200-71780000	Weak transcription	Duodenum Mucosa	Duodenum
34	chr11:71773200-71780000	Weak transcription	NH-A	brain
35	chr11:71773200-71783200	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr11:71773400-71779000	Weak transcription	HepG2	liver
37	chr11:71773400-71780000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr11:71773600-71780400	Weak transcription	Primary B cells from peripheral blood	blood
39	chr11:71773600-71783000	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr11:71774600-71779000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr11:71774600-71779800	Weak transcription	HMEC	breast
42	chr11:71774600-71780400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr11:71775800-71779000	Weak transcription	Fetal Intestine Small	intestine
44	chr11:71775800-71779000	Weak transcription	Fetal Stomach	stomach
45	chr11:71776000-71779400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr11:71776600-71779000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr11:71776600-71780200	Strong transcription	K562	blood
48	chr11:71776600-71783000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
49	chr11:71776800-71779200	Strong transcription	Primary hematopoietic stem cells	blood
50	chr11:71776800-71779400	Genic enhancers	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links