Variant report

Variant	rs4889548
Chromosome Location	chr16:31580530-31580531
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RAD21	chr16:31580030-31580530	H1-hESC	embryonic stem cell:	n/a	n/a

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C16orf58-6	chr16:31579088-31580845	NONHSAT141938
2	lnc-C16orf58-6	chr16:31579707-31580796	NONHSAT141939

Variant related genes	Relation type
ENSG00000261741	TF binding region

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11150626	0.92[JPT][hapmap]
rs13143	0.92[JPT][hapmap]
rs13337037	1.00[JPT][hapmap]
rs3934739	1.00[JPT][hapmap]
rs4519345	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4889673	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap]
rs6565236	1.00[JPT][hapmap]
rs6565242	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs8057401	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]
rs9934336	1.00[JPT][hapmap]
rs9935222	0.90[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv905747	chr16:31394179-31888684	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	123 gene(s)	inside rSNPs	diseases
2	nsv905750	chr16:31427678-31587662	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	98 gene(s)	inside rSNPs	diseases
3	nsv905753	chr16:31436932-31587662	Enhancers Active TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	97 gene(s)	inside rSNPs	diseases
4	nsv1060240	chr16:31495873-31581450	Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	esv3344221	chr16:31526786-31821640	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
6	esv3323903	chr16:31526802-31821640	Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	esv3504445	chr16:31526873-31821580	Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
8	esv3504446	chr16:31526873-31821580	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
9	esv3366795	chr16:31534951-31827424	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
10	nsv905755	chr16:31559220-31634221	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv905756	chr16:31559220-31647754	ZNF genes & repeats Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv905757	chr16:31565597-31634221	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	nsv905758	chr16:31565597-31647754	Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv905759	chr16:31565597-31647754	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv833195	chr16:31576112-31763222	ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4889548	AC026471.6	cis	lung	GTEx
rs4889548	AHSP	cis	parietal	SCAN
rs4889548	TAOK2	cis	parietal	SCAN
rs4889548	SLC5A2	cis	lung	GTEx

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:31579600-31581000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr16:31579600-31581000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
3	chr16:31579600-31581400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
4	chr16:31579800-31581000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
5	chr16:31579800-31581000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
6	chr16:31579800-31581200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
7	chr16:31579800-31581400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
8	chr16:31579800-31581400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr16:31580000-31580600	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
10	chr16:31580000-31580600	Bivalent Enhancer	Fetal Heart	heart
11	chr16:31580000-31580600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
12	chr16:31580000-31580600	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr16:31580000-31580800	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
14	chr16:31580000-31580800	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr16:31580000-31580800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr16:31580000-31580800	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr16:31580000-31580800	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
18	chr16:31580000-31580800	Bivalent/Poised TSS	Brain Substantia Nigra	brain
19	chr16:31580000-31580800	Bivalent/Poised TSS	Left Ventricle	heart
20	chr16:31580000-31581000	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr16:31580000-31581000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr16:31580000-31581000	Bivalent/Poised TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr16:31580000-31581000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
24	chr16:31580000-31581000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr16:31580000-31581000	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr16:31580000-31581000	Bivalent/Poised TSS	Adipose Nuclei	Adipose
27	chr16:31580000-31581000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
28	chr16:31580000-31581000	Active TSS	Duodenum Mucosa	Duodenum
29	chr16:31580000-31581000	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
30	chr16:31580000-31581000	Bivalent/Poised TSS	Psoas Muscle	Psoas
31	chr16:31580000-31581000	Bivalent/Poised TSS	HSMM	muscle
32	chr16:31580000-31581000	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
33	chr16:31580000-31581200	Bivalent/Poised TSS	ES-UCSF4 Cell Line	embryonic stem cell
34	chr16:31580000-31581200	Flanking Bivalent TSS/Enh	Cortex derived primary cultured neurospheres	brain
35	chr16:31580000-31581400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
36	chr16:31580000-31581400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr16:31580000-31581400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr16:31580000-31581400	Bivalent/Poised TSS	Brain Germinal Matrix	brain
39	chr16:31580200-31580600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr16:31580200-31580600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
41	chr16:31580200-31580600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
42	chr16:31580200-31580600	Active TSS	Primary hematopoietic stem cells short term culture	blood
43	chr16:31580200-31580600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
44	chr16:31580200-31580600	Bivalent/Poised TSS	Fetal Kidney	kidney
45	chr16:31580200-31580600	Bivalent/Poised TSS	Fetal Lung	lung
46	chr16:31580200-31580600	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
47	chr16:31580200-31580600	Bivalent/Poised TSS	Stomach Smooth Muscle	stomach
48	chr16:31580200-31580600	Bivalent/Poised TSS	HMEC	breast
49	chr16:31580200-31580800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
50	chr16:31580200-31580800	Active TSS	Rectal Mucosa Donor 31	rectum

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