Variant report

Variant	rs12599863
Chromosome Location	chr16:75593932-75593933
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:34)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:34 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr16:75593880-75594236	K562	blood:	n/a	n/a
2	TAF1	chr16:75593899-75594319	K562	blood:	n/a	n/a
3	ZNF384	chr16:75593355-75594427	K562	blood:	n/a	n/a
4	MYC	chr16:75593835-75594276	K562	blood:	n/a	n/a
5	TBP	chr16:75593565-75594343	K562	blood:	n/a	n/a
6	STAT5A	chr16:75593459-75593994	K562	blood:	n/a	n/a
7	YY1	chr16:75593741-75594242	K562	blood:	n/a	n/a
8	HEY1	chr16:75593793-75594230	K562	blood:	n/a	n/a
9	MAZ	chr16:75593568-75594267	K562	blood:	n/a	n/a
10	UBTF	chr16:75593644-75594308	K562	blood:	n/a	n/a
11	POLR2A	chr16:75593525-75594374	K562	blood:	n/a	n/a
12	HCFC1	chr16:75593580-75594251	K562	blood:	n/a	n/a
13	RCOR1	chr16:75593620-75594294	K562	blood:	n/a	n/a
14	EP300	chr16:75593622-75594335	K562	blood:	n/a	n/a
15	ZMIZ1	chr16:75593874-75594195	K562	blood:	n/a	n/a
16	CBX3	chr16:75593818-75594357	K562	blood:	n/a	n/a
17	ARID3A	chr16:75593627-75593953	K562	blood:	n/a	n/a
18	IRF1	chr16:75593722-75594323	K562	blood:	n/a	n/a
19	STAT5A	chr16:75593543-75594157	K562	blood:	n/a	n/a
20	HEY1	chr16:75593862-75594197	K562	blood:	n/a	n/a
21	TEAD4	chr16:75593477-75594303	K562	blood:	n/a	n/a
22	MAX	chr16:75593909-75594320	K562	blood:	n/a	n/a
23	POLR2A	chr16:75593829-75594241	ECC-1	luminal epithelium:	n/a	n/a
24	RCOR1	chr16:75593471-75594390	K562	blood:	n/a	n/a
25	POLR2A	chr16:75593876-75594277	K562	blood:	n/a	n/a
26	GTF2B	chr16:75593917-75594305	K562	blood:	n/a	n/a
27	TAF1	chr16:75593820-75594235	K562	blood:	n/a	n/a
28	POLR2A	chr16:75593874-75594335	K562	blood:	n/a	n/a
29	TBL1XR1	chr16:75593396-75594326	K562	blood:	n/a	n/a
30	POLR2A	chr16:75593822-75594257	K562	blood:	n/a	n/a
31	MAFK	chr16:75593900-75594300	K562	blood:	n/a	n/a
32	JUND	chr16:75593545-75594455	K562	blood:	n/a	n/a
33	POLR2A	chr16:75593823-75594330	K562	blood:	n/a	n/a
34	PML	chr16:75593764-75594286	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:75588622..75597419-chr16:75598326..75606239,14	K562	blood:
2	chr16:75587061..75591674-chr16:75591677..75597187,8	K562	blood:
3	chr16:75593028..75596412-chr16:75596623..75599848,3	MCF-7	breast:
4	chr16:75593216..75596661-chr16:75599139..75601757,3	MCF-7	breast:
5	chr16:75588642..75591639-chr16:75592315..75596973,4	MCF-7	breast:
6	chr16:75589157..75591789-chr16:75592246..75594958,4	K562	blood:
7	chr16:75593250..75596560-chr16:75613588..75617138,3	MCF-7	breast:
8	chr16:75587220..75591082-chr16:75591374..75595708,8	MCF-7	breast:

No data

Variant related genes	Relation type
TMEM231	TF binding region
ENSG00000205084	Chromatin interaction
ENSG00000034713	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1166206	0.81[ASN][1000 genomes]
rs12449192	0.82[AFR][1000 genomes]
rs2454866	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2550882	0.85[ASN][1000 genomes]
rs2550890	0.81[ASN][1000 genomes]
rs2550909	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2550913	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2572094	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2641801	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2641806	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2641808	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3863448	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4324157	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4887832	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4888435	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4888439	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59297469	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6564267	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7189895	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7195447	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8048944	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8061183	0.80[EUR][1000 genomes]
rs964632	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1065995	chr16:75373756-75626027	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
4	nsv1063718	chr16:75395969-75608071	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	nsv525955	chr16:75473332-75628345	Strong transcription Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
6	nsv457521	chr16:75487758-75603925	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
7	nsv572979	chr16:75487758-75603925	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
8	nsv532561	chr16:75519574-75636977	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
9	nsv906929	chr16:75569739-75594918	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs12599863	ADAT1	cis	Esophagus Muscularis	GTEx
rs12599863	ADAT1	cis	Skin Sun Exposed Lower leg	GTEx
rs12599863	ADAT1	cis	Adipose Subcutaneous	GTEx
rs12599863	ADAT1	cis	Muscle Skeletal	GTEx
rs12599863	ADAT1	cis	Esophagus Mucosa	GTEx
rs12599863	ADAT1	Cis_1M	lymphoblastoid	RTeQTL
rs12599863	ADAT1	cis	Artery Tibial	GTEx
rs12599863	ADAT1	cis	Thyroid	GTEx
rs12599863	ADAT1	cis	Nerve Tibial	GTEx
rs12599863	ADAT1	cis	lung	GTEx

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:75590600-75594000	Weak transcription	NH-A	brain
2	chr16:75590600-75595200	Weak transcription	GM12878-XiMat	blood
3	chr16:75590600-75599000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr16:75590800-75594000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr16:75591200-75594400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr16:75591200-75599400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr16:75592400-75594800	Enhancers	Placenta	Placenta
8	chr16:75592800-75594200	Enhancers	H1 Cell Line	embryonic stem cell
9	chr16:75592800-75594400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr16:75592800-75594400	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr16:75592800-75594400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr16:75592800-75594400	Enhancers	Placenta Amnion	Placenta Amnion
13	chr16:75593000-75594000	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr16:75593000-75594200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr16:75593000-75594200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
16	chr16:75593000-75594400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr16:75593000-75594400	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr16:75593000-75594600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr16:75593200-75594000	Weak transcription	Fetal Lung	lung
20	chr16:75593200-75594200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr16:75593200-75598600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr16:75593400-75594600	Enhancers	Fetal Muscle Leg	muscle
23	chr16:75593600-75594000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr16:75593600-75594000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr16:75593600-75594000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr16:75593600-75594000	Enhancers	Hela-S3	cervix
27	chr16:75593600-75594000	Enhancers	NHLF	lung
28	chr16:75593600-75594200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr16:75593600-75594200	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr16:75593600-75594400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr16:75593600-75594400	Enhancers	Muscle Satellite Cultured Cells	--
32	chr16:75593600-75594400	Enhancers	Adipose Nuclei	Adipose
33	chr16:75593600-75594400	Enhancers	HMEC	breast
34	chr16:75593600-75594400	Flanking Active TSS	K562	blood
35	chr16:75593600-75594400	Flanking Active TSS	Osteobl	bone
36	chr16:75593600-75594600	Enhancers	HSMM	muscle
37	chr16:75593600-75594600	Enhancers	NHDF-Ad	bronchial
38	chr16:75593800-75594000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr16:75593800-75594000	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr16:75593800-75594000	Enhancers	Cortex derived primary cultured neurospheres	brain
41	chr16:75593800-75594000	Flanking Active TSS	HSMMtube	muscle
42	chr16:75593800-75594200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr16:75593800-75594400	Enhancers	H9 Cell Line	embryonic stem cell
44	chr16:75593800-75594400	Enhancers	HUES64 Cell Line	embryonic stem cell
45	chr16:75593800-75594400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr16:75593800-75594400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr16:75593800-75594400	Enhancers	NHEK	skin
48	chr16:75593800-75594600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links