Variant report

Variant	rs11076560
Chromosome Location	chr16:48280404-48280405
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr16:47175994..47177897-chr16:48278487..48280949,2	MCF-7	breast:
2	chr16:48278224..48281613-chr16:48642327..48645557,3	MCF-7	breast:
3	chr16:48264506..48269686-chr16:48276668..48281172,8	MCF-7	breast:
4	chr16:48277878..48279864-chr16:48279870..48282600,2	K562	blood:

Variant related genes	Relation type
ENSG00000171208	Chromatin interaction
ENSG00000121270	Chromatin interaction
ENSG00000102910	Chromatin interaction
ENSG00000102921	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11076559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11554208	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12149826	0.85[MKK][hapmap]
rs13334798	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs17744321	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17750580	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17821664	1.00[GIH][hapmap]
rs17822471	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs17822697	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17825174	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs34505973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41282047	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56999468	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57251394	1.00[AFR][1000 genomes]
rs57879591	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59748923	0.89[AMR][1000 genomes]
rs7194667	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1059259	chr16:48113396-48304404	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv542916	chr16:48113396-48304404	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv1061316	chr16:48264175-48594219	Weak transcription Strong transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	esv1821072	chr16:48268318-48504364	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11076560	C2orf39	trans	brain	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:48277400-48281400	Active TSS	GM12878-XiMat	blood
2	chr16:48278000-48280600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr16:48278800-48280800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr16:48278800-48281800	Flanking Active TSS	Liver	Liver
5	chr16:48279000-48280600	Flanking Active TSS	Stomach Smooth Muscle	stomach
6	chr16:48279000-48287000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr16:48279200-48280600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr16:48279200-48280600	Enhancers	Stomach Mucosa	stomach
9	chr16:48279200-48280600	Flanking Active TSS	HepG2	liver
10	chr16:48279200-48280800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr16:48279200-48281600	Enhancers	Small Intestine	intestine
12	chr16:48279400-48280800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr16:48279400-48280800	Enhancers	Cortex derived primary cultured neurospheres	brain
14	chr16:48279400-48281000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr16:48279400-48281200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr16:48279400-48281600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr16:48279400-48281800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
18	chr16:48279400-48312600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr16:48279600-48280600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr16:48279600-48280600	Weak transcription	Lung	lung
21	chr16:48279600-48280800	Enhancers	Fetal Intestine Large	intestine
22	chr16:48279600-48280800	Enhancers	Fetal Intestine Small	intestine
23	chr16:48279600-48280800	Enhancers	Fetal Lung	lung
24	chr16:48279600-48280800	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr16:48279600-48281000	Enhancers	Primary T cells fromperipheralblood	blood
26	chr16:48279600-48281200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr16:48279600-48281200	Enhancers	Colon Smooth Muscle	Colon
28	chr16:48279600-48281200	Weak transcription	Gastric	stomach
29	chr16:48279600-48281200	Enhancers	Left Ventricle	heart
30	chr16:48279600-48281200	Weak transcription	Pancreas	Pancrea
31	chr16:48279600-48281400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr16:48279600-48281600	Enhancers	Primary B cells from peripheral blood	blood
33	chr16:48279600-48281600	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr16:48279600-48281600	Enhancers	Brain Substantia Nigra	brain
35	chr16:48279600-48281800	Enhancers	Primary T helper naive cells from peripheral blood	blood
36	chr16:48279600-48281800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr16:48279600-48281800	Enhancers	Brain Angular Gyrus	brain
38	chr16:48279600-48281800	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr16:48279600-48283000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr16:48279600-48283600	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr16:48279600-48285400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr16:48279600-48286400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr16:48279600-48286600	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr16:48279600-48286600	Weak transcription	Fetal Thymus	thymus
45	chr16:48279600-48287400	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr16:48279600-48292200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr16:48279600-48292600	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr16:48279600-48293400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr16:48279600-48293400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr16:48279600-48294200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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