Variant report

Variant	rs11039119
Chromosome Location	chr11:47201924-47201925
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr11:47201800-47201950	HRE	kidney:	n/a	n/a
2	POLR2A	chr11:47201619-47202451	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47196892..47202921-chr11:47278417..47285951,9	MCF-7	breast:
2	chr11:47196068..47203526-chr11:47288943..47293025,13	MCF-7	breast:
3	chr11:47201377..47203716-chr11:47267132..47269463,2	K562	blood:
4	chr11:47197774..47202059-chr11:47234538..47239113,7	MCF-7	breast:
5	chr11:47201513..47203398-chr11:47279251..47281417,2	MCF-7	breast:
6	chr11:47201336..47204009-chr11:47374499..47376871,2	MCF-7	breast:

No data

Variant related genes	Relation type
ARFGAP2	TF binding region
PACSIN3	TF binding region
ENSG00000110514	Chromatin interaction
ENSG00000134574	Chromatin interaction
ENSG00000025434	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs10466478	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10501319	0.83[CHB][hapmap];0.89[GIH][hapmap]
rs1055447	0.83[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs1060573	0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10769227	0.83[CHB][hapmap]
rs10769230	0.82[ASN][1000 genomes]
rs10769233	0.88[ASN][1000 genomes]
rs10769234	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs10769239	0.92[ASN][1000 genomes]
rs10838644	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs10838646	0.83[CHB][hapmap]
rs10838652	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs10838654	0.90[ASN][1000 genomes]
rs10838658	0.82[CHB][hapmap]
rs10838659	0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838660	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838662	0.83[CHB][hapmap];0.89[GIH][hapmap]
rs10838663	0.83[CHB][hapmap]
rs10838664	0.83[CHB][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs10838681	0.83[CHD][hapmap]
rs11039074	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs11039086	0.92[ASN][1000 genomes]
rs11039097	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039105	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039107	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039112	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039124	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039134	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11600668	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11601798	0.85[CHB][hapmap]
rs12224096	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12291341	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12417519	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs12574410	0.86[CHB][hapmap]
rs12796744	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12807887	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1872896	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1965952	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1976142	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1976143	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2018527	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2029298	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2087215	0.83[CHB][hapmap];0.89[GIH][hapmap]
rs2279438	0.83[CHB][hapmap]
rs2279439	0.83[CHB][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap]
rs4237547	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4319472	0.95[CEU][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4528282	0.82[CHB][hapmap]
rs4567413	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4579897	0.89[ASN][1000 genomes]
rs4587689	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs4752951	0.82[CHB][hapmap]
rs4752952	0.89[ASN][1000 genomes]
rs4752957	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4752962	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4752963	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4752965	0.83[CHB][hapmap]
rs4752967	0.95[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4752969	0.83[CHB][hapmap];0.89[GIH][hapmap]
rs4752971	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs57323109	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6485721	0.85[ASN][1000 genomes]
rs6485722	0.84[ASN][1000 genomes]
rs6485726	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs6485739	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7103581	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.88[ASN][1000 genomes]
rs7108902	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.88[ASN][1000 genomes]
rs7111270	0.83[CHB][hapmap]
rs7111764	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7112854	0.82[CHB][hapmap];0.86[GIH][hapmap]
rs7119952	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7121418	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7124648	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7125807	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.94[TSI][hapmap];0.85[ASN][1000 genomes]
rs7126005	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7128325	0.85[ASN][1000 genomes]
rs7128650	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7130006	0.83[CHB][hapmap];0.92[GIH][hapmap]
rs7130947	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs747650	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7479189	0.95[CEU][hapmap];0.89[ASN][1000 genomes]
rs7931260	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap]
rs7935346	0.86[GIH][hapmap]
rs7937101	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7937410	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs7937950	0.90[ASN][1000 genomes]
rs7940240	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs7942473	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7945315	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7946709	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];0.94[TSI][hapmap];0.90[ASN][1000 genomes]
rs7947878	0.81[ASN][1000 genomes]
rs7950753	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs923324	0.82[CHB][hapmap]
rs9633886	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11039119	C11orf49	cis	parietal	SCAN
rs11039119	DDB2	cis	Skin Sun Exposed Lower leg	GTEx
rs11039119	NUP160	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47197000-47207600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
2	chr11:47198800-47206400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:47199400-47202800	Genic enhancers	Fetal Muscle Trunk	muscle
4	chr11:47199400-47202800	Genic enhancers	Fetal Muscle Leg	muscle
5	chr11:47199400-47204000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
6	chr11:47199600-47202400	Strong transcription	iPS-15b Cell Line	embryonic stem cell
7	chr11:47199600-47202400	Genic enhancers	Right Ventricle	heart
8	chr11:47199600-47203200	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr11:47199600-47204200	Weak transcription	Thymus	Thymus
10	chr11:47199600-47204800	Strong transcription	Placenta Amnion	Placenta Amnion
11	chr11:47199600-47205600	Weak transcription	NHLF	lung
12	chr11:47199600-47206000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr11:47199600-47206600	Weak transcription	HUVEC	blood vessel
14	chr11:47199600-47206800	Weak transcription	Fetal Kidney	kidney
15	chr11:47199600-47207000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr11:47199800-47202000	Strong transcription	A549	lung
17	chr11:47199800-47202200	Strong transcription	Gastric	stomach
18	chr11:47199800-47202800	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:47199800-47203800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr11:47199800-47204800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:47199800-47204800	Strong transcription	Fetal Lung	lung
22	chr11:47199800-47205000	Weak transcription	Stomach Mucosa	stomach
23	chr11:47199800-47205200	Weak transcription	Fetal Thymus	thymus
24	chr11:47199800-47205600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr11:47199800-47205800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr11:47199800-47206000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:47199800-47206200	Strong transcription	NHEK	skin
28	chr11:47199800-47206400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr11:47199800-47206400	Weak transcription	Osteobl	bone
30	chr11:47200000-47203800	Weak transcription	Psoas Muscle	Psoas
31	chr11:47200000-47203800	Weak transcription	Right Atrium	heart
32	chr11:47200000-47203800	Weak transcription	Spleen	Spleen
33	chr11:47200000-47204200	Weak transcription	HSMMtube	muscle
34	chr11:47200000-47205000	Weak transcription	NHDF-Ad	bronchial
35	chr11:47200000-47205600	Weak transcription	Colonic Mucosa	Colon
36	chr11:47200000-47205600	Strong transcription	Fetal Stomach	stomach
37	chr11:47200000-47205800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr11:47200000-47205800	Weak transcription	Adipose Nuclei	Adipose
39	chr11:47200000-47205800	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr11:47200000-47206000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr11:47200000-47206200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr11:47200000-47206600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr11:47200000-47206600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr11:47200000-47207200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr11:47200200-47202400	Strong transcription	Esophagus	oesophagus
46	chr11:47200200-47203000	Strong transcription	H9 Cell Line	embryonic stem cell
47	chr11:47200200-47204400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr11:47200200-47204800	Strong transcription	Pancreas	Pancrea
49	chr11:47200200-47205600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr11:47200200-47206400	Weak transcription	Brain Inferior Temporal Lobe	brain

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