Variant report

Variant	rs4760687
Chromosome Location	chr12:48554258-48554259
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr12:48554213-48555189	PBDE	blood:	n/a	chr12:48554364-48554372

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr12:48554247-48554297	PANC-1	pancreas:	n/a
2	chr12:48554247-48554297	HMEC	breast:	n/a
3	chr12:48554247-48554297	NB4	blood:	n/a
4	chr12:48554247-48554297	HL-60	blood:	n/a
5	chr12:48554247-48554297	Hepatocyte	liver:	n/a
6	chr12:48554247-48554297	HPAEpiC	pulmonary alveolar:	n/a
7	chr12:48554247-48554297	HNPCEpiC	eye:	n/a
8	chr12:48554247-48554297	GM12878	blood:	n/a
9	chr12:48554247-48554297	Caco-2	colon:	n/a
10	chr12:48554247-48554297	RPTEC	kidney:	n/a
11	chr12:48554247-48554297	MCF10A-Er-Src	breast:	n/a
12	chr12:48554247-48554297	K562	blood:	n/a
13	chr12:48554247-48554297	HCF	heart:	n/a
14	chr12:48554247-48554297	HCM	heart:	n/a
15	chr12:48554247-48554297	U87	brain:	n/a
16	chr12:48554247-48554297	ovcar-3	ovarian:	n/a
17	chr12:48554247-48554297	CMK	blood:	n/a
18	chr12:48554247-48554297	NH-A	brain:	n/a
19	chr12:48554247-48554297	SK-N-SH_RA	brain:	n/a
20	chr12:48554247-48554297	SKMC	muscle:	n/a
21	chr12:48554247-48554297	HEK293	kidney:	embryo
22	chr12:48554247-48554297	ProgFib	skin:	n/a
23	chr12:48554247-48554297	H1-hESC	embryonic stem cell:	embryo
24	chr12:48554247-48554297	HEEpiC	esophagus:	n/a
25	chr12:48554247-48554297	SAEC	small airway:	n/a
26	chr12:48554247-48554297	BJ	skin:	n/a
27	chr12:48554247-48554297	AoSMC	blood vessel:	n/a
28	chr12:48554247-48554297	NT2-D1	testis:	n/a
29	chr12:48554247-48554297	HRPEpiC	eye:	n/a
30	chr12:48554247-48554297	NHBE	bronchial:	n/a
31	chr12:48554247-48554297	ECC-1	luminal epithelium:	n/a
32	chr12:48554247-48554297	HRCEpiC	kidney:	n/a
33	chr12:48554247-48554297	LNCaP	prostate:	n/a
34	chr12:48554247-48554297	PFSK-1	brain:	n/a
35	chr12:48554247-48554297	IMR90	lung:	fetal
36	chr12:48554247-48554297	AG04449	skin:	fetal
37	chr12:48554247-48554297	MCF-7	breast:	n/a
38	chr12:48554247-48554297	GM06990	blood:	n/a
39	chr12:48554247-48554297	BE2_C	brain:	n/a
40	chr12:48554247-48554297	HCT-116	colon:	n/a
41	chr12:48554247-48554297	HCPEpiC	choroid plexus:	n/a
42	chr12:48554247-48554297	HAEpiC	amniotic membrane:	n/a
43	chr12:48554247-48554297	HepG2	liver:	n/a
44	chr12:48554247-48554297	PrEC	prostate:	n/a
45	chr12:48554247-48554297	HUVEC	blood vessel:	n/a
46	chr12:48554247-48554297	HIPEpiC	eye:	n/a
47	chr12:48554247-48554297	GM12892	blood:	n/a
48	chr12:48554247-48554297	GM12891	blood:	n/a
49	chr12:48554247-48554297	SK-N-SH	brain:	n/a
50	chr12:48554247-48554297	Hela-S3	cervix:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48495831..48503326-chr12:48548997..48555180,8	K562	blood:

No data

Variant related genes	Relation type
ASB8	TF binding region
ASB8	CpG island
ENSG00000152556	Chromatin interaction
ENSG00000079387	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10082861	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10219623	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10219645	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10467101	0.83[CHB][hapmap];0.84[JPT][hapmap]
rs10875724	0.93[JPT][hapmap]
rs10875725	0.86[ASW][hapmap];0.83[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap]
rs10875732	1.00[JPT][hapmap]
rs10875745	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10875746	0.89[CHB][hapmap];0.94[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs10875747	0.87[ASN][1000 genomes]
rs10875748	0.87[ASN][1000 genomes]
rs10875750	0.94[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs10875756	0.97[ASN][1000 genomes]
rs10875762	0.88[ASN][1000 genomes]
rs10875764	0.81[ASN][1000 genomes]
rs10875767	0.83[CHB][hapmap];0.93[JPT][hapmap]
rs10875770	0.84[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs10875772	0.84[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs10875792	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs10875793	0.92[JPT][hapmap]
rs11168355	0.93[GIH][hapmap]
rs11168357	0.89[GIH][hapmap];0.93[JPT][hapmap]
rs11168369	1.00[JPT][hapmap]
rs11168371	0.88[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap]
rs11168403	1.00[JPT][hapmap]
rs11168413	0.87[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11168414	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11168415	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168416	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11168418	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs11168420	0.89[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11168421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11168422	0.87[ASN][1000 genomes]
rs11168425	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168427	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs11168433	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11168450	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11168459	0.84[CHB][hapmap];0.88[CHD][hapmap];0.93[JPT][hapmap]
rs11168516	0.87[JPT][hapmap]
rs11558768	0.89[ASN][1000 genomes]
rs12297470	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12304476	0.82[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs12305182	0.93[JPT][hapmap]
rs12305511	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12305647	0.86[ASN][1000 genomes]
rs12306290	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12306451	0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs12310813	0.91[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12312134	0.91[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1471997	0.86[JPT][hapmap]
rs17122666	0.89[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs17122812	0.84[CHB][hapmap];0.93[JPT][hapmap]
rs1859445	0.91[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2012773	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2079295	0.93[JPT][hapmap]
rs2107638	0.87[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2228500	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2269933	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.95[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2269935	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2269936	1.00[JPT][hapmap]
rs2279464	0.87[JPT][hapmap]
rs2286021	0.89[ASN][1000 genomes]
rs2634675	0.87[JPT][hapmap]
rs2732439	0.87[JPT][hapmap]
rs2732465	0.87[JPT][hapmap]
rs3185921	0.87[JPT][hapmap]
rs3751273	0.87[JPT][hapmap]
rs3782910	1.00[JPT][hapmap]
rs4760609	0.93[GIH][hapmap];0.93[JPT][hapmap]
rs4760619	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs4760622	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4760681	0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4760684	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4760689	0.97[ASN][1000 genomes]
rs4760690	0.97[ASN][1000 genomes]
rs4760695	0.94[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4760696	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs4760697	0.89[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs60106007	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61343568	0.84[ASN][1000 genomes]
rs6580659	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs7135779	0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs719008	0.93[JPT][hapmap]
rs725454	0.89[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs7299135	0.93[JPT][hapmap]
rs7299271	0.93[JPT][hapmap]
rs7485355	0.89[ASN][1000 genomes]
rs7486424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964359	0.81[CHB][hapmap]
rs8804	0.94[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs886588	0.85[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs9634261	0.87[JPT][hapmap]
rs989144	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS 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 miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv508673	chr12:48489786-48567138	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv8971	chr12:48536526-48758501	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
5	esv34439	chr12:48541757-48779562	Bivalent/Poised TSS Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	esv2757502	chr12:48547128-48779562	Genic enhancers Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4760687	RPAP3	cis	cerebellum	SCAN
rs4760687	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs4760687	RP1-228P16.1	cis	Thyroid	GTEx
rs4760687	RP1-228P16.1	cis	Artery Tibial	GTEx
rs4760687	C12orf41	cis	parietal	SCAN
rs4760687	AQP6	cis	parietal	SCAN
rs4760687	SENP1	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48551800-48554400	Weak transcription	Brain Germinal Matrix	brain
2	chr12:48552000-48554400	Weak transcription	Brain Anterior Caudate	brain
3	chr12:48552000-48554600	Weak transcription	Fetal Lung	lung
4	chr12:48552000-48554600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:48552000-48555800	Enhancers	Primary hematopoietic stem cells	blood
6	chr12:48552000-48556600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:48552000-48557800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr12:48552200-48554600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:48552200-48554600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr12:48552200-48554600	Weak transcription	Esophagus	oesophagus
11	chr12:48552200-48554600	Weak transcription	Fetal Thymus	thymus
12	chr12:48552200-48554600	Weak transcription	Psoas Muscle	Psoas
13	chr12:48552200-48554600	Weak transcription	K562	blood
14	chr12:48552200-48554800	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:48552200-48554800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
16	chr12:48552200-48556600	Enhancers	Skeletal Muscle Female	skeletal muscle
17	chr12:48552800-48554600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr12:48552800-48556000	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr12:48553200-48554600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr12:48553200-48554600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr12:48553800-48554400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:48553800-48555000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:48553800-48555400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr12:48553800-48555600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr12:48553800-48555600	Enhancers	GM12878-XiMat	blood
26	chr12:48554000-48554400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr12:48554000-48554800	Enhancers	Brain Hippocampus Middle	brain
28	chr12:48554000-48555200	Enhancers	Brain Cingulate Gyrus	brain
29	chr12:48554000-48555600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:48554000-48555600	Enhancers	Fetal Heart	heart
31	chr12:48554000-48555800	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr12:48554200-48555400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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