Variant report

Variant	rs6787500
Chromosome Location	chr3:48299439-48299440
allele	C/T
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	GATA3	chr3:48299386-48299649	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48298868..48300972-chr3:48308573..48310773,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CAMP-1	chr3:48299419-48299451	NONHSAT089547

Variant related genes	Relation type
MRPS18AP1	TF binding region

Extended variants
information (count: 139 )
Associated
traits (count: 51 )

rSNPs within LD-proxies of this variant (count:133)

rs_ID	r²[population]
rs1045482	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130162	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130163	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11130164	0.81[EUR][1000 genomes]
rs1134867	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11706221	0.80[EUR][1000 genomes]
rs11706277	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs11707997	0.80[EUR][1000 genomes]
rs11709691	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs11710257	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs11710861	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs11713476	0.89[EUR][1000 genomes]
rs11714176	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs11715799	0.81[EUR][1000 genomes]
rs11716371	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs11716848	0.80[EUR][1000 genomes]
rs11717716	0.80[EUR][1000 genomes]
rs11718329	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs11718350	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs11719365	0.83[EUR][1000 genomes]
rs11928691	0.85[EUR][1000 genomes]
rs13059037	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs13060020	0.80[EUR][1000 genomes]
rs13061269	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs13066044	0.80[EUR][1000 genomes]
rs13066758	0.83[EUR][1000 genomes]
rs13067450	0.83[EUR][1000 genomes]
rs13068265	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs13069029	0.82[EUR][1000 genomes]
rs13070210	0.82[EUR][1000 genomes]
rs13071960	0.81[EUR][1000 genomes]
rs13072018	0.85[EUR][1000 genomes]
rs13079728	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs13081169	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs13081633	0.82[EUR][1000 genomes]
rs13082859	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs13084616	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs13085251	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs13090538	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs13094727	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs13095983	0.82[EUR][1000 genomes]
rs13097450	0.84[EUR][1000 genomes]
rs13099560	0.96[YRI][hapmap]
rs13100815	0.83[EUR][1000 genomes]
rs17647717	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2125482	0.85[EUR][1000 genomes]
rs2541	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs3197223	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs34076262	0.81[EUR][1000 genomes]
rs34225441	0.83[EUR][1000 genomes]
rs34523942	0.83[EUR][1000 genomes]
rs34589064	0.83[EUR][1000 genomes]
rs34630841	0.83[EUR][1000 genomes]
rs34728236	0.83[EUR][1000 genomes]
rs34749846	0.83[EUR][1000 genomes]
rs34946886	0.83[EUR][1000 genomes]
rs35190747	0.83[EUR][1000 genomes]
rs35297395	0.83[EUR][1000 genomes]
rs35411187	0.82[EUR][1000 genomes]
rs35414021	0.83[EUR][1000 genomes]
rs35778847	0.83[EUR][1000 genomes]
rs35802497	0.83[EUR][1000 genomes]
rs35944878	0.84[EUR][1000 genomes]
rs36020562	0.82[EUR][1000 genomes]
rs36075665	0.83[EUR][1000 genomes]
rs36092070	0.86[EUR][1000 genomes]
rs36121690	0.83[EUR][1000 genomes]
rs3729577	0.87[CEU][hapmap]
rs3731513	0.87[CEU][hapmap]
rs3731555	0.88[CEU][hapmap]
rs3937	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs4130522	0.82[EUR][1000 genomes]
rs4130995	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4131361	0.85[EUR][1000 genomes]
rs4131362	0.85[EUR][1000 genomes]
rs4371540	0.82[EUR][1000 genomes]
rs4392440	0.83[EUR][1000 genomes]
rs4420898	0.80[EUR][1000 genomes]
rs4479622	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs4511915	0.83[EUR][1000 genomes]
rs4511916	0.83[EUR][1000 genomes]
rs4541431	0.81[EUR][1000 genomes]
rs4619808	0.81[EUR][1000 genomes]
rs4632568	0.81[EUR][1000 genomes]
rs6442110	1.00[CEU][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6442111	0.87[CEU][hapmap];0.86[EUR][1000 genomes]
rs6775179	0.86[EUR][1000 genomes]
rs6782166	0.82[EUR][1000 genomes]
rs6791930	0.91[CEU][hapmap];0.85[EUR][1000 genomes]
rs6793150	0.82[EUR][1000 genomes]
rs6793223	0.81[EUR][1000 genomes]
rs6793239	0.82[EUR][1000 genomes]
rs6794644	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6796343	0.84[EUR][1000 genomes]
rs6796490	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.84[EUR][1000 genomes]
rs6797587	0.81[CHB][hapmap];0.85[CHD][hapmap]
rs6800492	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs6801801	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs6804986	0.81[EUR][1000 genomes]
rs6806112	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71323391	0.84[EUR][1000 genomes]
rs71323394	0.82[EUR][1000 genomes]
rs71323395	0.80[EUR][1000 genomes]
rs71323397	0.80[EUR][1000 genomes]
rs7374376	0.93[YRI][hapmap]
rs745116	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs7614532	0.83[EUR][1000 genomes]
rs7617773	0.84[CHD][hapmap]
rs7619865	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7621785	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs7624450	0.83[EUR][1000 genomes]
rs7632297	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs7636461	0.84[EUR][1000 genomes]
rs7644414	0.81[EUR][1000 genomes]
rs7645425	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7648720	0.85[EUR][1000 genomes]
rs7652233	0.83[EUR][1000 genomes]
rs7653152	0.82[EUR][1000 genomes]
rs7653336	0.81[EUR][1000 genomes]
rs9311421	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs936426	0.87[CEU][hapmap]
rs936427	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs9818937	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs9819094	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9825637	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs9830016	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9833309	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9834095	0.85[EUR][1000 genomes]
rs9837228	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9846818	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9847953	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs9850672	0.84[CEU][hapmap];0.86[EUR][1000 genomes]
rs9853804	0.85[EUR][1000 genomes]

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	nsv529989	chr3:47909480-48301481	Genic enhancers Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1009243	chr3:47935331-48340448	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv536562	chr3:47935331-48340448	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv1002067	chr3:47996472-48326518	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS 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 miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv834682	chr3:48138137-48311122	Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv3339173	chr3:48292529-48302277	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:51)

SNP	Gene	Cis/trans	Tissue	Source
rs6787500	ARIH2	cis	parietal	SCAN
rs6787500	MRPS18AP1	cis	Esophagus Mucosa	GTEx
rs6787500	UQCRC1	cis	parietal	SCAN
rs6787500	ZNF589	cis	Cerebellum	GTEx
rs6787500	CDC25A	cis	Artery Tibial	GTEx
rs6787500	MRPS18AP1	cis	Esophagus Muscularis	GTEx
rs6787500	NME6	cis	Nerve Tibial	GTEx
rs6787500	ZNF589	cis	Adipose Subcutaneous	GTEx
rs6787500	MRPS18AP1	cis	Heart Left Ventricle	GTEx
rs6787500	ZNF589	cis	Thyroid	GTEx
rs6787500	NME6	cis	Artery Aorta	GTEx
rs6787500	FCF1P2	cis	Artery Tibial	GTEx
rs6787500	MRPS18AP1	cis	Artery Tibial	GTEx
rs6787500	ZNF589	cis	lung	GTEx
rs6787500	ZNF589	cis	Skin Sun Exposed Lower leg	GTEx
rs6787500	NME6	cis	multi-tissue	Pritchard
rs6787500	ALS2CL	cis	parietal	SCAN
rs6787500	CDC25A	cis	cerebellum	SCAN
rs6787500	NME6	cis	cerebellum	SCAN
rs6787500	NME6	cis	Artery Tibial	GTEx
rs6787500	ZNF589	cis	Esophagus Mucosa	GTEx
rs6787500	ZNF589	cis	Artery Tibial	GTEx
rs6787500	NME6	cis	lymphoblastoid	seeQTL
rs6787500	CDC25A	cis	Adipose Subcutaneous	GTEx
rs6787500	RBM5	cis	cerebellum	SCAN
rs6787500	ZNF589	cis	Temporal Cortex	GTEx
rs6787500	ZNF589	cis	Brain Pons	GTEx
rs6787500	ZNF589	cis	cerebellum	SCAN
rs6787500	MRPS18AP1	cis	Nerve Tibial	GTEx
rs6787500	ZNF589	Cis_1M	lymphoblastoid	RTeQTL
rs6787500	ZNF589	cis	Artery Aorta	GTEx
rs6787500	ZNF589	cis	Frontal Cortex	GTEx
rs6787500	NME6	cis	Skin Sun Exposed Lower leg	GTEx
rs6787500	MRPS18AP1	cis	Skin Sun Exposed Lower leg	GTEx
rs6787500	CDC25A	cis	Thyroid	GTEx
rs6787500	NME6	Cis_1M	lymphoblastoid	RTeQTL
rs6787500	ZNF589	cis	multi-tissue	Pritchard
rs6787500	MRPS18AP1	cis	Muscle Skeletal	GTEx
rs6787500	ZNF589	cis	Stomach	GTEx
rs6787500	CDC25A	cis	Muscle Skeletal	GTEx
rs6787500	MRPS18AP1	cis	Whole Blood	GTEx
rs6787500	MAP4	Cis_1M	lymphoblastoid	RTeQTL
rs6787500	ZNF589	cis	Whole Blood	GTEx
rs6787500	NME6	cis	Esophagus Muscularis	GTEx
rs6787500	MRPS18AP1	cis	lung	GTEx
rs6787500	ZNF589	cis	Nerve Tibial	GTEx
rs6787500	MRPS18AP1	cis	Thyroid	GTEx
rs6787500	ZNF589	cis	parietal	SCAN
rs6787500	MRPS18AP1	cis	Adipose Subcutaneous	GTEx
rs6787500	MRPS18AP1	cis	Artery Aorta	GTEx
rs6787500	MRPS18AP1	cis	Stomach	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48283200-48309800	Weak transcription	Fetal Lung	lung
2	chr3:48283400-48300400	Weak transcription	Gastric	stomach
3	chr3:48283400-48310000	Weak transcription	NH-A	brain
4	chr3:48283400-48315200	Weak transcription	Ovary	ovary
5	chr3:48283600-48300200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr3:48283600-48300800	Weak transcription	Colon Smooth Muscle	Colon
7	chr3:48283600-48309600	Weak transcription	Fetal Intestine Large	intestine
8	chr3:48283800-48307600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:48283800-48309400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr3:48283800-48310400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr3:48284200-48302800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr3:48285400-48303000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:48285600-48308200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr3:48285600-48312400	Weak transcription	Psoas Muscle	Psoas
15	chr3:48285800-48300200	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:48285800-48307600	Weak transcription	Pancreas	Pancrea
17	chr3:48285800-48310200	Weak transcription	Fetal Brain Male	brain
18	chr3:48285800-48311000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:48286400-48309400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:48288600-48312800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:48289200-48312000	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:48289200-48312600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:48289600-48306800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr3:48289800-48307800	Weak transcription	Brain Anterior Caudate	brain
25	chr3:48290000-48301400	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:48290000-48309400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr3:48290200-48300200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:48290400-48300400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr3:48290400-48300400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr3:48290400-48308200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr3:48290600-48299600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr3:48290600-48300000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr3:48290600-48307600	Weak transcription	HSMMtube	muscle
34	chr3:48291000-48308600	Weak transcription	HUVEC	blood vessel
35	chr3:48291200-48302800	Weak transcription	K562	blood
36	chr3:48291400-48299600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr3:48291400-48302200	Weak transcription	NHDF-Ad	bronchial
38	chr3:48291400-48302800	Weak transcription	Adipose Nuclei	Adipose
39	chr3:48291400-48303000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr3:48291400-48307600	Weak transcription	Brain Substantia Nigra	brain
41	chr3:48291600-48300400	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr3:48291600-48307600	Weak transcription	Left Ventricle	heart
43	chr3:48291800-48299600	Weak transcription	Liver	Liver
44	chr3:48292000-48300200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr3:48292400-48307000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:48292800-48309400	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr3:48293200-48302800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:48293200-48311400	Weak transcription	Placenta	Placenta
49	chr3:48293400-48300200	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr3:48293400-48300200	Weak transcription	Fetal Thymus	thymus

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