Variant report

Variant	rs4888441
Chromosome Location	chr16:75667013-75667014
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:13)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:13 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75664883-75667294	K562	blood:	n/a	n/a
2	FOXA1	chr16:75666607-75667315	HepG2	liver:	n/a	n/a
3	POLR2A	chr16:75665980-75667269	K562	blood:	n/a	n/a
4	RXRA	chr16:75666693-75667092	HepG2	liver:	n/a	n/a
5	POLR2A	chr16:75666165-75667154	HepG2	liver:	n/a	n/a
6	FOXA1	chr16:75666652-75667153	HepG2	liver:	n/a	n/a
7	POLR2A	chr16:75666984-75667290	GM12878	blood:	n/a	n/a
8	FOXA1	chr16:75666613-75667254	HepG2	liver:	n/a	n/a
9	SP1	chr16:75666707-75667167	HepG2	liver:	n/a	n/a
10	POLR2A	chr16:75664816-75667313	GM12878	blood:	n/a	n/a
11	FOXA1	chr16:75666702-75667204	HepG2	liver:	n/a	n/a
12	POLR2A	chr16:75666024-75667266	K562	blood:	n/a	n/a
13	FOXA2	chr16:75666716-75667156	HepG2	liver:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:75665889..75668271-chr16:75677726..75681584,4	MCF-7	breast:
2	chr16:75666708..75668853-chr16:75672275..75674428,2	MCF-7	breast:
3	chr16:75665324..75667854-chr16:75669001..75671047,2	MCF-7	breast:
4	chr16:75666197..75668073-chr16:75682009..75683733,2	K562	blood:

No data

Variant related genes	Relation type
KARS	TF binding region
ENSG00000166848	Chromatin interaction
ENSG00000065427	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10781978	0.86[ASN][1000 genomes]
rs11149843	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12596662	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1874022	1.00[CEU][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3743598	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3784929	0.84[CHB][hapmap]
rs3863448	0.85[CHD][hapmap];0.91[GIH][hapmap];0.80[MEX][hapmap];0.93[MKK][hapmap]
rs41505349	0.84[CHB][hapmap]
rs5010692	0.84[CHB][hapmap]
rs55864135	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61310184	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6564267	0.85[CHD][hapmap]
rs7189895	0.85[CHD][hapmap];0.91[GIH][hapmap];0.83[LWK][hapmap];0.93[MKK][hapmap]
rs964632	0.80[MEX][hapmap];0.87[MKK][hapmap];0.82[TSI][hapmap]

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	nsv916502	chr16:74845880-75732365	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	131 gene(s)	inside rSNPs	diseases
2	nsv931939	chr16:75261354-75765025	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	nsv532562	chr16:75614947-76371158	Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription 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 miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv1062010	chr16:75628562-75825725	Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
5	nsv1064880	chr16:75628562-75895699	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv542960	chr16:75628562-75895699	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
7	nsv1065543	chr16:75631306-75800170	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4888441	ADAT1	cis	multi-tissue	Pritchard
rs4888441	ADAT1	cis	lung	GTEx
rs4888441	ADAT1	cis	Adipose Subcutaneous	GTEx
rs4888441	ADAT1	cis	Esophagus Muscularis	GTEx
rs4888441	ADAT1	cis	Nerve Tibial	GTEx
rs4888441	ADAT1	cis	cerebellum	SCAN
rs4888441	ADAT1	cis	Esophagus Mucosa	GTEx
rs4888441	ADAT1	cis	Thyroid	GTEx
rs4888441	ADAT1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75656800-75667800	Weak transcription	Fetal Heart	heart
2	chr16:75657600-75668000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr16:75658400-75679200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr16:75658400-75679800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr16:75658400-75679800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr16:75658600-75678200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr16:75658800-75672400	Strong transcription	Fetal Brain Female	brain
8	chr16:75658800-75672600	Strong transcription	GM12878-XiMat	blood
9	chr16:75658800-75677000	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr16:75658800-75679800	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr16:75659000-75671800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr16:75659000-75672000	Strong transcription	Skeletal Muscle Male	skeletal muscle
13	chr16:75659000-75677000	Strong transcription	Brain Substantia Nigra	brain
14	chr16:75659000-75678200	Strong transcription	Fetal Muscle Leg	muscle
15	chr16:75659000-75678400	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr16:75659200-75675600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr16:75659200-75678000	Strong transcription	HepG2	liver
18	chr16:75659200-75680000	Strong transcription	Fetal Stomach	stomach
19	chr16:75659200-75680000	Strong transcription	A549	lung
20	chr16:75659200-75680600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr16:75659400-75668200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr16:75659400-75670600	Strong transcription	Brain Cingulate Gyrus	brain
23	chr16:75659400-75671400	Strong transcription	Fetal Lung	lung
24	chr16:75659400-75671800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr16:75659400-75671800	Strong transcription	Brain Germinal Matrix	brain
26	chr16:75659400-75672400	Strong transcription	Ovary	ovary
27	chr16:75659400-75674200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr16:75659400-75676800	Strong transcription	Fetal Muscle Trunk	muscle
29	chr16:75659400-75677200	Strong transcription	Muscle Satellite Cultured Cells	--
30	chr16:75659400-75678400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
31	chr16:75659400-75678400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr16:75659400-75679600	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr16:75659400-75680000	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr16:75659600-75667400	Strong transcription	Gastric	stomach
35	chr16:75659600-75668400	Strong transcription	Right Ventricle	heart
36	chr16:75659600-75670400	Strong transcription	NHLF	lung
37	chr16:75659600-75671400	Strong transcription	Brain Anterior Caudate	brain
38	chr16:75659600-75671600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr16:75659600-75671600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr16:75659600-75671600	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr16:75659600-75672000	Strong transcription	Brain Angular Gyrus	brain
42	chr16:75659600-75672000	Strong transcription	NHEK	skin
43	chr16:75659600-75672400	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr16:75659600-75675600	Strong transcription	HMEC	breast
45	chr16:75659600-75676800	Strong transcription	Left Ventricle	heart
46	chr16:75659600-75677000	Strong transcription	Brain Hippocampus Middle	brain
47	chr16:75659600-75678200	Strong transcription	Duodenum Mucosa	Duodenum
48	chr16:75659600-75678200	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr16:75659600-75678200	Strong transcription	Fetal Intestine Large	intestine
50	chr16:75659600-75678400	Strong transcription	Primary B cells from peripheral blood	blood

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