Variant report

Variant	rs2279439
Chromosome Location	chr11:47196982-47196983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47196953-47197152	GM12878	blood:	n/a	n/a
2	HCFC1	chr11:47196688-47200395	Hela-S3	cervix:	n/a	n/a
3	WRNIP1	chr11:47196922-47197911	GM12878	blood:	n/a	n/a
4	UBTF	chr11:47196973-47197039	K562	blood:	n/a	n/a
5	POLR2A	chr11:47196152-47201635	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr11:47196963-47197206	K562	blood:	n/a	n/a
7	POLR2A	chr11:47196647-47197062	GM12878	blood:	n/a	n/a
8	POLR2A	chr11:47196647-47196991	Hela-S3	cervix:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47196892..47202921-chr11:47278417..47285951,9	MCF-7	breast:
2	chr11:47195854..47197840-chr11:47393831..47395541,2	K562	blood:
3	chr11:47195816..47200318-chr11:47289518..47292814,8	K562	blood:
4	chr11:47195231..47200543-chr11:47288487..47293127,12	MCF-7	breast:
5	chr11:47157651..47159882-chr11:47195629..47197785,2	K562	blood:
6	chr11:47196838..47200214-chr11:47234555..47238435,7	MCF-7	breast:
7	chr11:47196068..47203526-chr11:47288943..47293025,13	MCF-7	breast:
8	chr11:47194502..47201735-chr11:47289181..47294156,14	K562	blood:
9	chr11:46866389..46868370-chr11:47196689..47198841,3	MCF-7	breast:
10	chr11:47196939..47199221-chr11:47446629..47449473,2	K562	blood:

No data

Variant related genes	Relation type
ARFGAP2	TF binding region
ENSG00000256746	Chromatin interaction
ENSG00000149179	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000175216	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000165916	Chromatin interaction
ENSG00000247675	Chromatin interaction

Extended variants
information (count: 102 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10466478	0.83[CHB][hapmap]
rs10501319	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1055447	0.84[GIH][hapmap]
rs1060573	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs10742797	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10769225	0.80[ASN][1000 genomes]
rs10769226	0.82[ASN][1000 genomes]
rs10769227	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs10769228	0.83[ASN][1000 genomes]
rs10769234	0.86[CHB][hapmap]
rs10769248	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10838640	0.82[ASN][1000 genomes]
rs10838641	0.83[ASN][1000 genomes]
rs10838644	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.93[TSI][hapmap];0.85[ASN][1000 genomes]
rs10838646	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10838652	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838658	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10838660	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs10838662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.96[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838663	1.00[CHB][hapmap];0.92[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10838664	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.87[YRI][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11039074	0.90[CHB][hapmap]
rs11039080	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11039081	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11039097	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs11039098	0.82[ASN][1000 genomes]
rs11039105	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs11039112	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs11039119	0.83[CHB][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap]
rs11600668	0.83[CHB][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs11601798	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11603373	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12224096	0.82[CHB][hapmap]
rs12417519	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12574410	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs12796744	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs1872896	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs2029298	0.89[GIH][hapmap]
rs2087215	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2279438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3758666	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3758667	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3922684	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4269876	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4315028	0.90[ASN][1000 genomes]
rs4394802	0.80[ASN][1000 genomes]
rs4494268	0.95[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.84[ASN][1000 genomes]
rs4498951	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4528282	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs4548577	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4567413	0.89[GIH][hapmap]
rs4576779	0.93[ASN][1000 genomes]
rs4587689	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4752815	0.80[ASN][1000 genomes]
rs4752816	0.80[ASN][1000 genomes]
rs4752951	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4752957	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs4752962	0.83[CHB][hapmap]
rs4752965	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.95[ASN][1000 genomes]
rs4752967	0.83[CHB][hapmap]
rs4752968	0.86[ASN][1000 genomes]
rs4752969	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61896133	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61896136	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61897787	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61897844	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61897857	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6485715	0.80[ASN][1000 genomes]
rs6485726	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6485739	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7103581	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7108822	0.91[CEU][hapmap];0.87[ASN][1000 genomes]
rs7108902	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7111270	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7112854	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7114683	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7121418	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7123632	0.82[ASN][1000 genomes]
rs7124648	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.87[ASN][1000 genomes]
rs7125807	0.82[CHB][hapmap];0.86[GIH][hapmap]
rs7126005	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.87[ASN][1000 genomes]
rs7127741	0.91[CEU][hapmap];0.89[ASN][1000 genomes]
rs7128650	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.87[ASN][1000 genomes]
rs7130006	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7130947	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.80[ASN][1000 genomes]
rs747650	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7929688	0.80[ASN][1000 genomes]
rs7931260	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7935346	0.82[CEU][hapmap];0.83[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.82[ASN][1000 genomes]
rs7937101	0.89[GIH][hapmap]
rs7937410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7938169	0.80[ASN][1000 genomes]
rs7939786	0.80[ASN][1000 genomes]
rs7940240	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945315	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7946709	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7950753	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.93[TSI][hapmap];0.88[ASN][1000 genomes]
rs7951979	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs901747	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs923324	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.95[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	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv897324	chr11:47193566-47212032	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2279439	NUP160	cis	cerebellum	SCAN
rs2279439	C11orf49	cis	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47175400-47197600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47178000-47197000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr11:47181400-47197000	Weak transcription	Right Atrium	heart
4	chr11:47182200-47197000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr11:47183200-47197000	Strong transcription	Placenta	Placenta
6	chr11:47183200-47197200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:47183400-47197000	Strong transcription	Cortex derived primary cultured neurospheres	brain
8	chr11:47183400-47197000	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr11:47183400-47197000	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:47183600-47197000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr11:47183600-47197000	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr11:47184400-47197000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr11:47184800-47197000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr11:47185400-47197000	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr11:47185400-47197200	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr11:47185600-47197000	Strong transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:47185600-47197000	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr11:47185600-47197000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
19	chr11:47185600-47197000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr11:47185600-47197000	Strong transcription	HSMM	muscle
21	chr11:47185600-47197000	Strong transcription	Osteobl	bone
22	chr11:47186000-47197000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr11:47188600-47197400	Weak transcription	Psoas Muscle	Psoas
24	chr11:47189800-47197000	Weak transcription	Small Intestine	intestine
25	chr11:47192800-47197000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr11:47192800-47197000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
27	chr11:47193000-47197000	Genic enhancers	Brain Substantia Nigra	brain
28	chr11:47193000-47197200	Genic enhancers	Brain Angular Gyrus	brain
29	chr11:47193000-47197200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
30	chr11:47193000-47197400	Genic enhancers	Primary T cells fromperipheralblood	blood
31	chr11:47193800-47197000	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr11:47193800-47197000	Genic enhancers	Liver	Liver
33	chr11:47193800-47197000	Genic enhancers	Duodenum Smooth Muscle	Duodenum
34	chr11:47193800-47197200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
35	chr11:47193800-47197200	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr11:47194000-47197200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
37	chr11:47194000-47197400	Genic enhancers	Primary B cells from peripheral blood	blood
38	chr11:47194200-47197000	Genic enhancers	Stomach Smooth Muscle	stomach
39	chr11:47194200-47197200	Genic enhancers	Fetal Muscle Trunk	muscle
40	chr11:47194200-47197200	Genic enhancers	Fetal Thymus	thymus
41	chr11:47194800-47197200	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr11:47195200-47197000	Strong transcription	HSMMtube	muscle
43	chr11:47195200-47197200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr11:47195400-47197400	Weak transcription	Aorta	Aorta
45	chr11:47195600-47197000	Weak transcription	Stomach Mucosa	stomach
46	chr11:47195600-47197200	Weak transcription	Esophagus	oesophagus
47	chr11:47195800-47197000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr11:47195800-47197000	Weak transcription	NH-A	brain
49	chr11:47195800-47197400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr11:47196000-47197000	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links