Variant report

Variant	rs2279238
Chromosome Location	chr11:47282024-47282025
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	chr11:47197631..47199665-chr11:47279516..47282212,2	K562	blood:
2	chr11:47206745..47208837-chr11:47280102..47282885,2	K562	blood:
3	chr11:47196892..47202921-chr11:47278417..47285951,9	MCF-7	breast:
4	chr11:47205835..47208468-chr11:47280225..47282817,2	MCF-7	breast:
5	chr11:47197941..47200223-chr11:47281634..47284173,2	K562	blood:
6	chr11:47279843..47284326-chr11:47288675..47293634,16	MCF-7	breast:
7	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
8	chr11:47268496..47273681-chr11:47277782..47283365,10	K562	blood:
9	chr11:47183256..47186030-chr11:47281970..47284554,2	MCF-7	breast:
10	chr11:47277979..47283267-chr11:47289057..47293509,9	K562	blood:
11	chr11:47267134..47271941-chr11:47277592..47282899,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000110514	Chromatin interaction
ENSG00000165912	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000256746	Chromatin interaction
ENSG00000149182	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1051006	0.93[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.88[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1052373	0.82[MEX][hapmap]
rs10742797	0.81[JPT][hapmap]
rs10769253	0.80[CEU][hapmap];0.90[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10769254	0.81[AMR][1000 genomes]
rs10769255	0.87[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs10838663	1.00[CEU][hapmap]
rs10838681	0.82[CHB][hapmap];0.86[MEX][hapmap]
rs10838685	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10838686	0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10838687	0.88[ASW][hapmap];0.95[MEX][hapmap];0.92[AMR][1000 genomes]
rs10838689	0.81[ASW][hapmap];0.80[CEU][hapmap];0.93[GIH][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10838692	0.82[MEX][hapmap]
rs11039144	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039148	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11039155	0.97[EUR][1000 genomes]
rs11039189	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11493249	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11530166	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12222581	0.81[AMR][1000 genomes]
rs12574081	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12574410	1.00[CEU][hapmap]
rs1449626	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1449627	0.82[MEX][hapmap]
rs16938581	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2242261	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2242262	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2254240	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2290146	0.94[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2290148	0.94[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2305280	0.88[ASW][hapmap]
rs2306353	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2596398	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2633080	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2633083	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2957873	0.94[ASW][hapmap];0.82[MEX][hapmap];0.83[YRI][hapmap]
rs326224	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3729802	0.85[CEU][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3729804	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3729805	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3758670	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3781619	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.93[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3781620	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3824866	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4647725	0.84[EUR][1000 genomes]
rs4647726	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4647737	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4647741	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4647754	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4752965	1.00[CEU][hapmap]
rs4752972	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4752973	0.94[ASW][hapmap];0.82[CHB][hapmap];0.80[CHD][hapmap];1.00[MEX][hapmap];0.83[YRI][hapmap]
rs4752977	0.94[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.88[TSI][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4752978	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4752979	0.88[AMR][1000 genomes]
rs4752983	1.00[ASW][hapmap];0.80[CEU][hapmap];0.81[CHD][hapmap];0.90[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58023804	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs59567949	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6485751	0.88[AMR][1000 genomes]
rs7118396	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7120118	0.82[MEX][hapmap]
rs7120158	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7124958	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7395496	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.82[EUR][1000 genomes]
rs753992	0.80[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs753993	0.82[AMR][1000 genomes]
rs7928073	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7933246	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs830083	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs830084	1.00[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs830085	0.82[MEX][hapmap]

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	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2279238	PTPMT1	cis	parietal	SCAN
rs2279238	ACP2	cis	Thyroid	GTEx
rs2279238	DDB2	cis	lymphoblastoid	seeQTL
rs2279238	ACP2	cis	lymphoblastoid	seeQTL
rs2279238	ACP2	Cis_1M	lymphoblastoid	RTeQTL
rs2279238	DDB2	Cis_1M	lymphoblastoid	RTeQTL
rs2279238	NR1H3	cis	multi-tissue	Pritchard
rs2279238	ACP2	cis	multi-tissue	Pritchard

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47272400-47286400	Weak transcription	Dnd41	blood
2	chr11:47275800-47286800	Weak transcription	Primary T cells from cord blood	blood
3	chr11:47278800-47282200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr11:47278800-47282200	Flanking Active TSS	Adipose Nuclei	Adipose
5	chr11:47279200-47288800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr11:47279400-47286800	Weak transcription	NHEK	skin
7	chr11:47279400-47289400	Weak transcription	Fetal Brain Female	brain
8	chr11:47279800-47287000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr11:47279800-47289800	Weak transcription	Esophagus	oesophagus
10	chr11:47280000-47282800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr11:47280000-47289400	Weak transcription	Brain Angular Gyrus	brain
12	chr11:47280000-47289600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr11:47280000-47290000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:47280200-47282200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:47280200-47282200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr11:47280200-47282800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr11:47280200-47289400	Weak transcription	Pancreas	Pancrea
18	chr11:47280200-47289600	Weak transcription	Brain Substantia Nigra	brain
19	chr11:47280200-47289800	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr11:47280200-47289800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr11:47280200-47290600	Weak transcription	Ovary	ovary
22	chr11:47280200-47290800	Weak transcription	Aorta	Aorta
23	chr11:47280600-47289800	Weak transcription	Fetal Kidney	kidney
24	chr11:47280800-47282200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr11:47281000-47284800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr11:47281000-47285800	Weak transcription	Osteobl	bone
27	chr11:47281000-47286200	Weak transcription	NHDF-Ad	bronchial
28	chr11:47281000-47289800	Weak transcription	Fetal Brain Male	brain
29	chr11:47281000-47290800	Weak transcription	Small Intestine	intestine
30	chr11:47281200-47283600	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr11:47281200-47285800	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr11:47281200-47285800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr11:47281200-47286200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr11:47281200-47286800	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr11:47281200-47289000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr11:47281200-47289200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr11:47281200-47289400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr11:47281200-47289400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:47281200-47289400	Weak transcription	Fetal Lung	lung
40	chr11:47281200-47290000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr11:47281400-47282200	Enhancers	Primary hematopoietic stem cells	blood
42	chr11:47281400-47282200	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr11:47281400-47282800	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr11:47281400-47284400	Weak transcription	K562	blood
45	chr11:47281400-47285800	Weak transcription	NHLF	lung
46	chr11:47281400-47288800	Weak transcription	Placenta	Placenta
47	chr11:47281400-47289400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr11:47281400-47289600	Weak transcription	Brain Hippocampus Middle	brain
49	chr11:47281600-47282200	Weak transcription	Right Ventricle	heart
50	chr11:47281600-47282600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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