Variant report

Variant	rs2885880
Chromosome Location	chr11:71655847-71655848
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:71650756..71652380-chr11:71654533..71657023,3	K562	blood:
2	chr11:71654518..71657892-chr11:71675208..71678197,3	MCF-7	breast:
3	chr11:71653405..71656260-chr11:71657576..71659642,2	MCF-7	breast:
4	chr11:71641143..71643109-chr11:71654078..71656466,2	MCF-7	breast:
5	chr11:71648762..71653405-chr11:71655542..71658221,6	MCF-7	breast:
6	chr11:71654014..71655958-chr11:71656574..71658856,2	MCF-7	breast:
7	chr11:71636451..71639692-chr11:71654710..71658319,3	MCF-7	breast:
8	chr11:71639007..71647132-chr11:71654924..71662463,14	MCF-7	breast:
9	chr11:71644522..71646628-chr11:71653948..71656589,2	MCF-7	breast:
10	chr11:71627212..71629834-chr11:71654212..71656346,2	MCF-7	breast:
11	chr11:71655022..71660498-chr11:71666064..71670761,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000255296	Chromatin interaction
ENSG00000137522	Chromatin interaction
ENSG00000254469	Chromatin interaction

Extended variants
information (count: 194 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:190)

rs_ID	r²[population]
rs10128658	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10501408	0.83[JPT][hapmap]
rs1055452	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs1057992	0.83[JPT][hapmap]
rs10736781	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10736782	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10736783	0.84[JPT][hapmap]
rs10736786	0.83[EUR][1000 genomes]
rs10751189	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10751190	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10751191	0.85[JPT][hapmap]
rs10793011	0.85[JPT][hapmap]
rs10793016	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10898814	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10898817	0.81[ASN][1000 genomes]
rs12293885	0.81[JPT][hapmap]
rs1541304	0.85[JPT][hapmap]
rs1541306	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1548348	0.83[JPT][hapmap]
rs1573500	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1573501	0.85[JPT][hapmap]
rs1573502	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1612492	0.81[EUR][1000 genomes]
rs1629046	0.83[EUR][1000 genomes]
rs1629722	0.81[EUR][1000 genomes]
rs1783959	0.83[EUR][1000 genomes]
rs1783960	0.81[EUR][1000 genomes]
rs1783961	0.81[EUR][1000 genomes]
rs1783962	0.81[EUR][1000 genomes]
rs1791449	0.81[EUR][1000 genomes]
rs1791450	0.81[EUR][1000 genomes]
rs1791452	0.81[EUR][1000 genomes]
rs1892919	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1892920	0.84[JPT][hapmap]
rs1892921	0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1894003	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1894004	0.83[JPT][hapmap]
rs1939242	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1939243	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1939245	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1939247	0.80[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2155142	0.83[JPT][hapmap]
rs2155145	0.84[JPT][hapmap]
rs2187496	1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2276384	0.83[JPT][hapmap]
rs2298456	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2363736	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2460254	0.81[EUR][1000 genomes]
rs2503	0.83[JPT][hapmap]
rs2508856	0.83[JPT][hapmap]
rs2511099	0.81[EUR][1000 genomes]
rs2845856	0.81[EUR][1000 genomes]
rs2845857	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3016291	0.81[EUR][1000 genomes]
rs3018301	0.81[EUR][1000 genomes]
rs3018310	0.83[JPT][hapmap]
rs3814721	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3886589	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4121395	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4338555	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4387373	0.85[JPT][hapmap]
rs4477459	0.85[JPT][hapmap]
rs4479013	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4491255	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs474231	0.86[EUR][1000 genomes]
rs475959	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs479487	0.81[EUR][1000 genomes]
rs481300	0.81[EUR][1000 genomes]
rs481355	0.81[EUR][1000 genomes]
rs493065	0.81[JPT][hapmap]
rs4943821	0.81[EUR][1000 genomes]
rs4944232	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4944242	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4944243	0.85[JPT][hapmap]
rs4944258	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4944259	0.82[ASN][1000 genomes]
rs4945340	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4945353	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4945378	0.85[JPT][hapmap]
rs4945392	0.83[JPT][hapmap]
rs4945426	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4945434	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4945435	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs495567	0.81[EUR][1000 genomes]
rs499386	0.83[EUR][1000 genomes]
rs506395	0.81[EUR][1000 genomes]
rs510925	0.85[JPT][hapmap]
rs513292	0.81[EUR][1000 genomes]
rs514431	0.86[EUR][1000 genomes]
rs519098	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs529522	0.83[EUR][1000 genomes]
rs529567	0.81[EUR][1000 genomes]
rs531326	0.81[EUR][1000 genomes]
rs532433	0.81[EUR][1000 genomes]
rs548127	0.81[EUR][1000 genomes]
rs550230	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs552966	0.81[JPT][hapmap]
rs556089	0.81[EUR][1000 genomes]
rs558859	0.86[EUR][1000 genomes]
rs55972015	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56097487	0.86[AFR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs562414	0.81[EUR][1000 genomes]
rs562469	0.81[EUR][1000 genomes]
rs562621	0.81[EUR][1000 genomes]
rs566965	0.81[EUR][1000 genomes]
rs567026	0.83[JPT][hapmap]
rs573227	0.81[EUR][1000 genomes]
rs575831	0.82[JPT][hapmap]
rs575871	0.83[JPT][hapmap]
rs577435	0.83[JPT][hapmap]
rs579320	0.81[JPT][hapmap]
rs585228	0.81[JPT][hapmap]
rs595062	0.85[JPT][hapmap]
rs596130	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs599611	0.81[EUR][1000 genomes]
rs607319	0.81[EUR][1000 genomes]
rs607446	0.81[JPT][hapmap]
rs610004	0.81[JPT][hapmap]
rs610041	0.81[JPT][hapmap]
rs612255	0.85[JPT][hapmap]
rs613140	0.81[EUR][1000 genomes]
rs613535	0.81[EUR][1000 genomes]
rs613971	0.81[EUR][1000 genomes]
rs615000	0.81[JPT][hapmap]
rs618186	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs629714	0.81[EUR][1000 genomes]
rs642573	0.81[JPT][hapmap]
rs642618	0.81[JPT][hapmap];0.81[EUR][1000 genomes]
rs654780	0.81[EUR][1000 genomes]
rs656990	0.81[EUR][1000 genomes]
rs657819	0.81[EUR][1000 genomes]
rs658699	0.81[EUR][1000 genomes]
rs6592447	0.83[JPT][hapmap]
rs6592448	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6592449	0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6592450	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6592451	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6592452	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6592453	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6592455	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6592456	0.85[JPT][hapmap]
rs6592458	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs661242	0.83[EUR][1000 genomes]
rs661290	0.85[JPT][hapmap]
rs662649	0.81[EUR][1000 genomes]
rs674688	0.81[EUR][1000 genomes]
rs680150	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs686205	0.81[EUR][1000 genomes]
rs686340	0.84[JPT][hapmap]
rs693648	0.81[EUR][1000 genomes]
rs7101701	0.83[EUR][1000 genomes]
rs7102192	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7103210	0.81[JPT][hapmap];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7106730	0.85[CHB][hapmap];0.93[JPT][hapmap]
rs7106748	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7113436	0.83[JPT][hapmap]
rs7115513	0.85[JPT][hapmap]
rs7116495	0.83[EUR][1000 genomes]
rs7121080	0.85[JPT][hapmap]
rs7121260	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7123992	1.00[CEU][hapmap];0.86[JPT][hapmap]
rs7124000	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7126394	0.85[JPT][hapmap]
rs7127865	0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7128317	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7128346	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7128974	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73531952	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7480015	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7924516	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7924834	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs7925411	0.83[JPT][hapmap]
rs7925604	0.85[JPT][hapmap]
rs7925901	0.88[ASN][1000 genomes]
rs7926533	0.81[EUR][1000 genomes]
rs7930142	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7930544	0.81[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7930721	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7930722	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7931941	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7937515	0.86[JPT][hapmap]
rs7937582	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7943227	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7944073	0.81[EUR][1000 genomes]
rs7948821	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7949480	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7951194	0.93[ASN][1000 genomes]
rs947932	0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs949323	0.83[JPT][hapmap]
rs949325	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	esv2758276	chr11:71363639-71657576	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv2759836	chr11:71363639-71657576	Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2885880	NUMA1	Cis_1M	lymphoblastoid	RTeQTL
rs2885880	NUMA1	cis	uninvolved skin	skin_eQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71641000-71671000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr11:71641200-71670800	Weak transcription	Fetal Muscle Trunk	muscle
3	chr11:71641200-71671400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr11:71641400-71658000	Weak transcription	Lung	lung
5	chr11:71641400-71661600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:71641400-71670800	Weak transcription	Esophagus	oesophagus
7	chr11:71641400-71671000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:71641400-71671000	Weak transcription	Fetal Thymus	thymus
9	chr11:71641400-71671400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr11:71641600-71656800	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr11:71641600-71658000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:71641600-71659600	Weak transcription	Fetal Kidney	kidney
13	chr11:71641600-71670800	Weak transcription	Spleen	Spleen
14	chr11:71641600-71671400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr11:71641600-71671600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr11:71641600-71671600	Weak transcription	Brain Germinal Matrix	brain
17	chr11:71641600-71671600	Weak transcription	Brain Hippocampus Middle	brain
18	chr11:71641600-71673400	Weak transcription	NHLF	lung
19	chr11:71641800-71671600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:71642400-71671000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr11:71642400-71671000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr11:71642600-71671000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:71642600-71671200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr11:71642800-71671200	Weak transcription	Dnd41	blood
25	chr11:71642800-71671400	Weak transcription	Fetal Brain Female	brain
26	chr11:71644200-71665600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr11:71645400-71659000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr11:71645600-71658400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:71645600-71658400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr11:71645600-71659600	Weak transcription	Gastric	stomach
31	chr11:71645600-71671200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr11:71645800-71660200	Weak transcription	Thymus	Thymus
33	chr11:71645800-71660800	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr11:71645800-71671400	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr11:71646000-71656600	Weak transcription	Fetal Intestine Small	intestine
36	chr11:71646000-71658400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr11:71646600-71658000	Weak transcription	Fetal Intestine Large	intestine
38	chr11:71646600-71658000	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:71648400-71659400	Weak transcription	Ovary	ovary
40	chr11:71648800-71671600	Weak transcription	Rectal Smooth Muscle	rectum
41	chr11:71649000-71658800	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr11:71649000-71659600	Weak transcription	Fetal Lung	lung
43	chr11:71649000-71662600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr11:71649200-71658400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr11:71649200-71658400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr11:71649200-71659600	Weak transcription	Left Ventricle	heart
47	chr11:71649200-71662400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
48	chr11:71649200-71666400	Weak transcription	Primary B cells from cord blood	blood
49	chr11:71649200-71670800	Weak transcription	Fetal Stomach	stomach
50	chr11:71649200-71671000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links