Variant report

Variant	rs656640
Chromosome Location	chr11:71781710-71781711
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFIC	chr11:71780842-71782015	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr11:71780787..71782950-chr11:71789834..71792937,3	MCF-7	breast:
2	chr11:71780121..71782648-chr11:72143336..72145276,2	K562	blood:
3	chr11:71743810..71760160-chr11:71777190..71805714,79	MCF-7	breast:
4	chr11:71749103..71754368-chr11:71778297..71785639,14	MCF-7	breast:
5	chr11:71779732..71781998-chr11:71797035..71799576,2	K562	blood:
6	chr11:71781171..71786362-chr11:71787519..71793039,9	K562	blood:
7	chr11:71780985..71784804-chr11:71822969..71825529,4	K562	blood:

No data

Variant related genes	Relation type
NUMA1	TF binding region
ENSG00000212089	Chromatin interaction
ENSG00000206783	Chromatin interaction
ENSG00000184154	Chromatin interaction
ENSG00000162129	Chromatin interaction
ENSG00000110200	Chromatin interaction
ENSG00000137497	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs10128658	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10736786	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10751190	0.85[EUR][1000 genomes]
rs10751193	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10793016	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10898814	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10898817	0.83[ASN][1000 genomes]
rs11235440	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12272213	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12283462	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12293885	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1541306	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1573500	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1573502	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17161966	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17161980	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17161991	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1791544	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1806778	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1892919	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1892921	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1894003	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1939242	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1939243	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1939245	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1939247	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2250866	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2298456	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2511074	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2511075	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2511076	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2511078	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2511079	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2511114	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2511116	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2511121	0.83[ASN][1000 genomes]
rs2511122	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2845857	0.90[EUR][1000 genomes]
rs28504107	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3018301	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3018304	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3018308	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3133230	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3133233	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3750908	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3793938	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3814721	0.85[EUR][1000 genomes]
rs3886589	0.81[EUR][1000 genomes]
rs4121395	0.81[EUR][1000 genomes]
rs4338555	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4479013	0.81[EUR][1000 genomes]
rs482013	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs493065	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4943821	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4944242	0.81[EUR][1000 genomes]
rs4944258	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4944259	0.87[ASN][1000 genomes]
rs4945426	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4945434	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4945435	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs495567	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs510925	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs517837	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs541022	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542752	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs547208	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs548961	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs552966	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs560777	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56097487	0.83[EUR][1000 genomes]
rs57025151	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs585228	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58991229	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs597513	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs598835	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs607446	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs610004	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs610041	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs615000	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs627329	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs636946	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs642573	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs642618	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6592448	0.81[EUR][1000 genomes]
rs6592449	0.81[EUR][1000 genomes]
rs6592451	0.81[EUR][1000 genomes]
rs6592453	0.85[EUR][1000 genomes]
rs6592455	0.85[EUR][1000 genomes]
rs6592458	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6592459	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs659513	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs670802	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs671681	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs673478	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs675185	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs676721	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs677279	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs678193	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs679926	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7101701	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7113549	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7116188	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7116495	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7121260	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7123102	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7124000	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7126838	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7127865	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7128317	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7128974	0.85[EUR][1000 genomes]
rs73531952	0.85[EUR][1000 genomes]
rs73539529	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73539532	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73543609	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73543633	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7480015	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7924516	0.81[EUR][1000 genomes]
rs7930142	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7930544	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7930721	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7930722	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7937515	0.83[ASN][1000 genomes]
rs7937582	0.88[ASN][1000 genomes]
rs7949480	0.85[EUR][1000 genomes]
rs947932	0.81[EUR][1000 genomes]
rs949325	0.85[EUR][1000 genomes];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	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
rs656640	NUMA1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:71754200-71789600	Weak transcription	Fetal Brain Female	brain
2	chr11:71755400-71783000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr11:71756200-71783200	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:71757000-71783200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr11:71767400-71786400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr11:71770000-71783200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:71771600-71789800	Weak transcription	Fetal Brain Male	brain
8	chr11:71773200-71783200	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:71773600-71783000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr11:71776600-71783000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr11:71777400-71783000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr11:71778400-71789800	Weak transcription	Brain Germinal Matrix	brain
13	chr11:71779200-71784600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr11:71779200-71786200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr11:71779400-71783000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr11:71779400-71784400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr11:71779400-71790200	Weak transcription	Thymus	Thymus
18	chr11:71779600-71781800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr11:71779600-71782000	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr11:71779600-71782000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
21	chr11:71779800-71782200	Flanking Active TSS	GM12878-XiMat	blood
22	chr11:71780000-71781800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr11:71780000-71781800	Enhancers	Brain Anterior Caudate	brain
24	chr11:71780000-71781800	Flanking Active TSS	Osteobl	bone
25	chr11:71780000-71782000	Enhancers	ES-I3 Cell Line	embryonic stem cell
26	chr11:71780000-71782000	Enhancers	Duodenum Mucosa	Duodenum
27	chr11:71780000-71782400	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr11:71780000-71783400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr11:71780200-71781800	Enhancers	Colonic Mucosa	Colon
30	chr11:71780200-71781800	Genic enhancers	NHEK	skin
31	chr11:71780200-71782200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
32	chr11:71780200-71782200	Enhancers	Placenta Amnion	Placenta Amnion
33	chr11:71780200-71782200	Genic enhancers	K562	blood
34	chr11:71780200-71784800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr11:71780200-71785000	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr11:71780400-71781800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr11:71780400-71781800	Enhancers	Aorta	Aorta
38	chr11:71780400-71781800	Enhancers	Fetal Intestine Small	intestine
39	chr11:71780400-71781800	Enhancers	Left Ventricle	heart
40	chr11:71780400-71781800	Enhancers	Right Atrium	heart
41	chr11:71780400-71782000	Enhancers	Primary B cells from peripheral blood	blood
42	chr11:71780400-71782000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr11:71780400-71782000	Enhancers	Fetal Muscle Leg	muscle
44	chr11:71780400-71782000	Enhancers	Placenta	Placenta
45	chr11:71780400-71782000	Enhancers	Ovary	ovary
46	chr11:71780400-71782000	Enhancers	Stomach Mucosa	stomach
47	chr11:71780400-71782200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr11:71780400-71782200	Enhancers	Brain Substantia Nigra	brain
49	chr11:71780400-71782200	Enhancers	Fetal Kidney	kidney
50	chr11:71780400-71782200	Enhancers	Fetal Stomach	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links