Variant report

Variant	rs4404082
Chromosome Location	chr16:79750512-79750513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:79744125..79746553-chr16:79748554..79750825,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MAF-2	chr16:79749256-79750737	XLOC_012017
2	lnc-MAF-2	chr16:79749256-79750737	XLOC_012017
3	lnc-MAF-2	chr16:79748640-79750737	XLOC_012017
4	lnc-MAF-2	chr16:79749256-79750737	XLOC_012017

Extended variants
information (count: 15 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11642757	0.85[EUR][1000 genomes]
rs11642836	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17767281	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4340340	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62043313	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7189954	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7194711	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7196490	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7199794	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7203910	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv573285	chr16:79158182-80127326	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv906992	chr16:79649394-79769790	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv530714	chr16:79661581-79925435	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv833296	chr16:79692236-79889727	Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv833297	chr16:79732501-79920419	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4404082	AK000792	cis	multi-tissue	Pritchard
rs4404082	RP11-345M22.2	cis	Thyroid	GTEx
rs4404082	RP11-345M22.2	cis	Adipose Subcutaneous	GTEx
rs4404082	RP11-345M22.2	cis	Skin Sun Exposed Lower leg	GTEx
rs4404082	HSS00332776	cis	multi-tissue	Pritchard

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:79746800-79751600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr16:79747000-79750600	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr16:79747000-79751800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr16:79747800-79750800	Enhancers	Ovary	ovary
5	chr16:79748000-79756200	Weak transcription	Gastric	stomach
6	chr16:79748200-79760400	Enhancers	Fetal Intestine Small	intestine
7	chr16:79748400-79752200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr16:79748400-79752200	Enhancers	Fetal Lung	lung
9	chr16:79748400-79752400	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr16:79748400-79760800	Enhancers	Fetal Intestine Large	intestine
11	chr16:79749000-79750600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr16:79749000-79754800	Weak transcription	Colon Smooth Muscle	Colon
13	chr16:79749200-79750600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr16:79749400-79751600	Enhancers	Aorta	Aorta
15	chr16:79749400-79751800	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr16:79749800-79750600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr16:79749800-79754000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr16:79749800-79754400	Weak transcription	Liver	Liver
19	chr16:79749800-79754800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr16:79749800-79756400	Weak transcription	Stomach Mucosa	stomach
21	chr16:79750000-79752000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr16:79750200-79751200	Enhancers	HSMMtube	muscle
23	chr16:79750200-79751400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr16:79750200-79752000	Enhancers	Primary hematopoietic stem cells	blood
25	chr16:79750200-79752400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr16:79750400-79751000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr16:79750400-79751000	Enhancers	Fetal Heart	heart
28	chr16:79750400-79752000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr16:79750400-79752200	Enhancers	Fetal Kidney	kidney
30	chr16:79750400-79752200	Enhancers	Fetal Muscle Leg	muscle

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