Variant report

Variant	rs60988480
Chromosome Location	chr16:75661084-75661085
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:26)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:26 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75658658-75661263	GM12878	blood:	n/a	n/a
2	POLR2A	chr16:75660674-75661346	K562	blood:	n/a	n/a
3	POLR2A	chr16:75660767-75661232	H1-hESC	embryonic stem cell:	n/a	n/a
4	POLR2A	chr16:75660493-75661440	GM12892	blood:	n/a	n/a
5	POLR2A	chr16:75659575-75661350	HepG2	liver:	n/a	n/a
6	POLR2A	chr16:75660659-75661320	HepG2	liver:	n/a	n/a
7	POLR2A	chr16:75658339-75662100	K562	blood:	n/a	n/a
8	POLR2A	chr16:75659512-75661313	GM12878	blood:	n/a	n/a
9	POLR2A	chr16:75659396-75661359	GM12891	blood:	n/a	n/a
10	POLR2A	chr16:75660606-75661350	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr16:75660506-75661346	GM12891	blood:	n/a	n/a
12	POLR2A	chr16:75659485-75661464	GM12892	blood:	n/a	n/a
13	POLR2A	chr16:75660557-75661318	HepG2	liver:	n/a	n/a
14	POLR2A	chr16:75660751-75661224	K562	blood:	n/a	n/a
15	POLR2A	chr16:75660956-75661459	GM12891	blood:	n/a	n/a
16	POLR2A	chr16:75658427-75661240	Hela-S3	cervix:	n/a	n/a
17	POLR2A	chr16:75659356-75661414	GM12878	blood:	n/a	n/a
18	POLR2A	chr16:75660361-75661266	K562	blood:	n/a	n/a
19	POLR2A	chr16:75658750-75661468	GM12892	blood:	n/a	n/a
20	POLR2A	chr16:75660816-75661300	K562	blood:	n/a	n/a
21	POLR2A	chr16:75659354-75661366	GM12892	blood:	n/a	n/a
22	POLR2A	chr16:75661073-75661238	GM12878	blood:	n/a	n/a
23	POLR2A	chr16:75659353-75661250	K562	blood:	n/a	n/a
24	POLR2A	chr16:75658438-75661358	K562	blood:	n/a	n/a
25	POLR2A	chr16:75659545-75661204	A549	lung:	n/a	n/a
26	POLR2A	chr16:75658173-75661283	HepG2	liver:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:75653410..75664044-chr16:75674901..75683254,27	MCF-7	breast:
2	chr16:75656276..75657906-chr16:75659788..75662087,2	K562	blood:
3	chr16:75655386..75658646-chr16:75660355..75663332,4	MCF-7	breast:
4	chr16:75589260..75591107-chr16:75659674..75662120,3	K562	blood:
5	chr16:75589260..75591065-chr16:75659818..75662120,2	K562	blood:
6	chr16:75654016..75659144-chr16:75660095..75666421,8	K562	blood:

No data

Variant related genes	Relation type
ADAT1	TF binding region
ENSG00000065427	Chromatin interaction
ENSG00000205084	Chromatin interaction
ENSG00000065457	Chromatin interaction
ENSG00000166848	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11149840	0.85[EUR][1000 genomes]
rs11149841	0.89[ASN][1000 genomes]
rs11642599	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11645180	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11649388	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3743604	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3784932	0.80[EUR][1000 genomes]
rs4149500	0.86[EUR][1000 genomes]
rs4149501	0.85[EUR][1000 genomes]
rs4149504	0.81[EUR][1000 genomes]
rs4485400	0.85[EUR][1000 genomes]
rs7202717	0.85[EUR][1000 genomes]
rs7206481	0.86[EUR][1000 genomes]
rs74024804	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8048818	0.81[EUR][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	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
rs60988480	ADAT1	cis	Artery Tibial	GTEx
rs60988480	ADAT1	cis	Thyroid	GTEx
rs60988480	ADAT1	cis	lung	GTEx
rs60988480	ADAT1	cis	multi-tissue	Pritchard
rs60988480	ADAT1	cis	Esophagus Muscularis	GTEx
rs60988480	ADAT1	cis	Skin Sun Exposed Lower leg	GTEx
rs60988480	ADAT1	Cis_1M	lymphoblastoid	RTeQTL
rs60988480	ADAT1	cis	Adipose Subcutaneous	GTEx
rs60988480	ADAT1	cis	Muscle Skeletal	GTEx

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	chr16:75657400-75661600	Weak transcription	Small Intestine	intestine
3	chr16:75657600-75661800	Weak transcription	Colonic Mucosa	Colon
4	chr16:75657600-75666200	Weak transcription	Fetal Brain Male	brain
5	chr16:75657600-75668000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr16:75657800-75661800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr16:75657800-75661800	Weak transcription	NHDF-Ad	bronchial
8	chr16:75658400-75679200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr16:75658400-75679800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:75658400-75679800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr16:75658600-75678200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr16:75658800-75672400	Strong transcription	Fetal Brain Female	brain
13	chr16:75658800-75672600	Strong transcription	GM12878-XiMat	blood
14	chr16:75658800-75677000	Strong transcription	H1 Cell Line	embryonic stem cell
15	chr16:75658800-75679800	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr16:75659000-75662000	Strong transcription	Primary B cells from cord blood	blood
17	chr16:75659000-75662000	Strong transcription	Dnd41	blood
18	chr16:75659000-75671800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr16:75659000-75672000	Strong transcription	Skeletal Muscle Male	skeletal muscle
20	chr16:75659000-75677000	Strong transcription	Brain Substantia Nigra	brain
21	chr16:75659000-75678200	Strong transcription	Fetal Muscle Leg	muscle
22	chr16:75659000-75678400	Strong transcription	Skeletal Muscle Female	skeletal muscle
23	chr16:75659200-75675600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr16:75659200-75678000	Strong transcription	HepG2	liver
25	chr16:75659200-75680000	Strong transcription	Fetal Stomach	stomach
26	chr16:75659200-75680000	Strong transcription	A549	lung
27	chr16:75659200-75680600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr16:75659400-75668200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr16:75659400-75670600	Strong transcription	Brain Cingulate Gyrus	brain
30	chr16:75659400-75671400	Strong transcription	Fetal Lung	lung
31	chr16:75659400-75671800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr16:75659400-75671800	Strong transcription	Brain Germinal Matrix	brain
33	chr16:75659400-75672400	Strong transcription	Ovary	ovary
34	chr16:75659400-75674200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr16:75659400-75676800	Strong transcription	Fetal Muscle Trunk	muscle
36	chr16:75659400-75677200	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr16:75659400-75678400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr16:75659400-75678400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr16:75659400-75679600	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr16:75659400-75680000	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr16:75659600-75661800	Strong transcription	Adipose Nuclei	Adipose
42	chr16:75659600-75661800	Strong transcription	Thymus	Thymus
43	chr16:75659600-75662200	Strong transcription	Spleen	Spleen
44	chr16:75659600-75666200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr16:75659600-75667400	Strong transcription	Gastric	stomach
46	chr16:75659600-75668400	Strong transcription	Right Ventricle	heart
47	chr16:75659600-75670400	Strong transcription	NHLF	lung
48	chr16:75659600-75671400	Strong transcription	Brain Anterior Caudate	brain
49	chr16:75659600-75671600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr16:75659600-75671600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links