Variant report

Variant	rs10838664
Chromosome Location	chr11:47203904-47203905
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47203732..47205768-chr11:47206390..47208181,2	MCF-7	breast:
2	chr11:47202119..47205492-chr11:47206060..47209673,5	K562	blood:
3	chr11:47203683..47208496-chr11:47223862..47228000,5	MCF-7	breast:
4	chr11:47202498..47205214-chr11:47434945..47437570,2	K562	blood:
5	chr11:47201336..47204009-chr11:47374499..47376871,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000266540	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000165915	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10466478	0.83[CHB][hapmap]
rs10501319	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[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];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10769226	0.81[ASN][1000 genomes]
rs10769227	0.82[ASN][1000 genomes]
rs10769228	0.82[ASN][1000 genomes]
rs10769234	0.86[CHB][hapmap]
rs10769248	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10838640	0.81[ASN][1000 genomes]
rs10838641	0.82[ASN][1000 genomes]
rs10838644	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap];0.84[ASN][1000 genomes]
rs10838646	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10838652	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.88[ASN][1000 genomes]
rs10838658	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10838660	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs10838662	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10838663	1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11039074	0.90[CHB][hapmap]
rs11039080	0.88[ASN][1000 genomes]
rs11039081	0.90[ASN][1000 genomes]
rs11039097	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs11039098	0.81[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];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs11600668	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs11601798	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11603373	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12224096	0.82[CHB][hapmap]
rs12417519	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.92[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	0.80[CHD][hapmap];0.89[GIH][hapmap]
rs2087215	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2279438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279439	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]
rs3758666	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3758667	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3781619	0.82[CHD][hapmap]
rs3922684	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4269876	0.92[ASN][1000 genomes]
rs4315028	0.90[ASN][1000 genomes]
rs4463814	0.85[AFR][1000 genomes]
rs4494268	0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs4498951	0.92[ASN][1000 genomes]
rs4528282	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs4548577	0.82[ASN][1000 genomes]
rs4567413	0.80[CHD][hapmap];0.89[GIH][hapmap]
rs4576779	0.92[ASN][1000 genomes]
rs4587689	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.92[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];0.87[CHD][hapmap];0.95[JPT][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];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.96[TSI][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61896133	0.92[ASN][1000 genomes]
rs61896136	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61897787	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61897844	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61897857	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6485726	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.88[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]
rs7112854	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7114683	0.88[ASN][1000 genomes]
rs7121418	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7123632	0.81[ASN][1000 genomes]
rs7124648	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.90[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];0.82[MEX][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs7127741	0.91[CEU][hapmap];0.88[ASN][1000 genomes]
rs7128650	0.89[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs7130006	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs747650	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7931260	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7935346	0.82[CEU][hapmap];0.83[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.90[TSI][hapmap];0.82[ASN][1000 genomes]
rs7937101	0.80[CHD][hapmap];0.89[GIH][hapmap]
rs7937410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7940240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.87[ASN][1000 genomes]
rs7951979	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs901747	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs923324	0.93[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[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
rs10838664	NUP160	cis	cerebellum	SCAN
rs10838664	DDB2	cis	parietal	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	chr11:47199400-47204000	Transcr. at gene 5' and 3'	Skeletal Muscle Female	skeletal muscle
4	chr11:47199600-47204200	Weak transcription	Thymus	Thymus
5	chr11:47199600-47204800	Strong transcription	Placenta Amnion	Placenta Amnion
6	chr11:47199600-47205600	Weak transcription	NHLF	lung
7	chr11:47199600-47206000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:47199600-47206600	Weak transcription	HUVEC	blood vessel
9	chr11:47199600-47206800	Weak transcription	Fetal Kidney	kidney
10	chr11:47199600-47207000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:47199800-47204800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr11:47199800-47204800	Strong transcription	Fetal Lung	lung
13	chr11:47199800-47205000	Weak transcription	Stomach Mucosa	stomach
14	chr11:47199800-47205200	Weak transcription	Fetal Thymus	thymus
15	chr11:47199800-47205600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr11:47199800-47205800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:47199800-47206000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr11:47199800-47206200	Strong transcription	NHEK	skin
19	chr11:47199800-47206400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr11:47199800-47206400	Weak transcription	Osteobl	bone
21	chr11:47200000-47204200	Weak transcription	HSMMtube	muscle
22	chr11:47200000-47205000	Weak transcription	NHDF-Ad	bronchial
23	chr11:47200000-47205600	Weak transcription	Colonic Mucosa	Colon
24	chr11:47200000-47205600	Strong transcription	Fetal Stomach	stomach
25	chr11:47200000-47205800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr11:47200000-47205800	Weak transcription	Adipose Nuclei	Adipose
27	chr11:47200000-47205800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr11:47200000-47206000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr11:47200000-47206200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr11:47200000-47206600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr11:47200000-47206600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:47200000-47207200	Weak transcription	Primary hematopoietic stem cells	blood
33	chr11:47200200-47204400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:47200200-47204800	Strong transcription	Pancreas	Pancrea
35	chr11:47200200-47205600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr11:47200200-47206400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr11:47200200-47206800	Weak transcription	Dnd41	blood
38	chr11:47200400-47205000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr11:47200400-47207200	Weak transcription	K562	blood
40	chr11:47201200-47204000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr11:47201400-47205200	Strong transcription	Placenta	Placenta
42	chr11:47201600-47204000	Strong transcription	Fetal Intestine Large	intestine
43	chr11:47201600-47204000	Strong transcription	Fetal Intestine Small	intestine
44	chr11:47201600-47204400	Strong transcription	HepG2	liver
45	chr11:47201600-47205600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr11:47201600-47206000	Weak transcription	NH-A	brain
47	chr11:47201600-47206400	Enhancers	Fetal Heart	heart
48	chr11:47201800-47204000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr11:47201800-47204600	Strong transcription	Hela-S3	cervix
50	chr11:47201800-47205600	Weak transcription	Brain Angular Gyrus	brain

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