Variant report

Variant	rs4788460
Chromosome Location	chr16:72154509-72154510
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11640722	0.87[GIH][hapmap]
rs11647069	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11648622	0.84[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.89[ASN][1000 genomes]
rs17604349	0.83[GIH][hapmap]
rs3812985	0.87[GIH][hapmap]
rs4788605	0.87[GIH][hapmap]
rs4788614	0.83[GIH][hapmap]
rs5467	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs5477	1.00[YRI][hapmap]
rs55741258	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	esv2758430	chr16:71976344-72274347	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	esv2758654	chr16:71976344-72274347	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv428329	chr16:71976344-72274347	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
6	nsv534588	chr16:72078262-72287230	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4788460	NAE1	cis	parietal	SCAN
rs4788460	LRRC36	cis	parietal	SCAN
rs4788460	ABCC4	trans	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72142800-72158600	Weak transcription	Fetal Brain Male	brain
2	chr16:72145800-72156000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr16:72145800-72160400	Weak transcription	HMEC	breast
4	chr16:72146400-72158600	Weak transcription	Colon Smooth Muscle	Colon
5	chr16:72146400-72159000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr16:72146600-72154600	Weak transcription	HUVEC	blood vessel
7	chr16:72146600-72155000	Weak transcription	Stomach Mucosa	stomach
8	chr16:72146600-72159000	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr16:72146600-72159200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr16:72146600-72166600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr16:72146800-72158400	Weak transcription	HepG2	liver
12	chr16:72146800-72158600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr16:72146800-72159000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr16:72146800-72159200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr16:72147000-72155600	Weak transcription	NHEK	skin
16	chr16:72147000-72158600	Weak transcription	Ovary	ovary
17	chr16:72147000-72158800	Weak transcription	HUES6 Cell Line	embryonic stem cell
18	chr16:72147000-72158800	Weak transcription	Brain Angular Gyrus	brain
19	chr16:72147000-72159000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr16:72147000-72164800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr16:72147000-72172200	Weak transcription	Dnd41	blood
22	chr16:72147200-72158600	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr16:72147200-72158600	Weak transcription	Brain Substantia Nigra	brain
24	chr16:72147200-72158600	Weak transcription	GM12878-XiMat	blood
25	chr16:72147200-72158800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr16:72147200-72159000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr16:72147200-72159000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr16:72147200-72159000	Weak transcription	Fetal Lung	lung
29	chr16:72147200-72159200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr16:72147400-72158200	Weak transcription	Spleen	Spleen
31	chr16:72147400-72158600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr16:72147400-72158800	Weak transcription	Fetal Thymus	thymus
33	chr16:72147400-72159000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr16:72147400-72159000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr16:72147400-72159000	Weak transcription	Duodenum Mucosa	Duodenum
36	chr16:72147400-72159000	Weak transcription	Fetal Brain Female	brain
37	chr16:72147400-72159000	Weak transcription	Stomach Smooth Muscle	stomach
38	chr16:72147400-72159200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr16:72147400-72159200	Weak transcription	Pancreas	Pancrea
40	chr16:72147400-72162200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr16:72147400-72164800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr16:72147600-72158400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr16:72147600-72158400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr16:72147600-72158600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr16:72147600-72158800	Weak transcription	Rectal Smooth Muscle	rectum
46	chr16:72147600-72159000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr16:72147600-72159000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr16:72147600-72159000	Weak transcription	Colonic Mucosa	Colon
49	chr16:72147600-72159200	Weak transcription	Lung	lung
50	chr16:72147600-72165000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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