Variant report

Variant	rs11130318
Chromosome Location	chr3:52734954-52734955
allele	C/G
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	POLR2A	chr3:52733568-52735088	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:52734891-52734968	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52733044..52735275-chr3:52738797..52740602,3	MCF-7	breast:

Variant related genes	Relation type
SPCS1	TF binding region
GLT8D1	TF binding region
ENSG00000016864	Chromatin interaction
ENSG00000114902	Chromatin interaction

Extended variants
information (count: 164 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:163)

rs_ID	r²[population]
rs1029871	0.80[EUR][1000 genomes]
rs10433615	0.83[EUR][1000 genomes]
rs10780035	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10865973	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10865974	0.85[EUR][1000 genomes]
rs11130307	0.83[EUR][1000 genomes]
rs11130308	0.81[EUR][1000 genomes]
rs11130310	0.83[EUR][1000 genomes]
rs11130311	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11130312	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11130313	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11130314	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11130315	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11130317	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11130319	0.83[EUR][1000 genomes]
rs11130321	0.84[EUR][1000 genomes]
rs11130323	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11130325	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11130327	0.80[EUR][1000 genomes]
rs11177	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11708075	0.86[EUR][1000 genomes]
rs11709448	0.85[EUR][1000 genomes]
rs11714030	0.84[EUR][1000 genomes]
rs11714088	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11714419	0.86[EUR][1000 genomes]
rs11716747	0.83[EUR][1000 genomes]
rs11717043	0.85[EUR][1000 genomes]
rs11718509	0.81[EUR][1000 genomes]
rs11719514	0.84[EUR][1000 genomes]
rs11720432	0.86[EUR][1000 genomes]
rs12486554	0.85[EUR][1000 genomes]
rs12486847	0.88[EUR][1000 genomes]
rs12487445	0.83[EUR][1000 genomes]
rs12487591	0.84[EUR][1000 genomes]
rs12488461	0.88[EUR][1000 genomes]
rs12488527	0.84[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12493107	0.87[EUR][1000 genomes]
rs12496476	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12496634	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12498066	0.85[EUR][1000 genomes]
rs12632265	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12632381	0.83[EUR][1000 genomes]
rs12635140	0.85[EUR][1000 genomes]
rs13060675	0.86[EUR][1000 genomes]
rs13061253	0.84[AFR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13064064	0.85[EUR][1000 genomes]
rs13065019	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13065851	0.85[EUR][1000 genomes]
rs13068293	0.85[EUR][1000 genomes]
rs13069481	0.85[EUR][1000 genomes]
rs13074853	0.80[EUR][1000 genomes]
rs13076193	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13079063	0.83[EUR][1000 genomes]
rs13081031	0.87[EUR][1000 genomes]
rs13082208	0.84[EUR][1000 genomes]
rs13082960	0.83[EUR][1000 genomes]
rs13085331	0.85[EUR][1000 genomes]
rs13085775	0.83[EUR][1000 genomes]
rs13085895	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs13086297	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13086898	0.86[EUR][1000 genomes]
rs13087772	0.83[EUR][1000 genomes]
rs13095332	0.81[EUR][1000 genomes]
rs1468638	0.83[EUR][1000 genomes]
rs1561337	0.85[EUR][1000 genomes]
rs17264436	0.82[EUR][1000 genomes]
rs1866268	0.85[EUR][1000 genomes]
rs2028216	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2072390	0.80[EUR][1000 genomes]
rs2079929	0.84[EUR][1000 genomes]
rs2109634	0.83[EUR][1000 genomes]
rs2118540	0.85[EUR][1000 genomes]
rs2159644	0.80[EUR][1000 genomes]
rs2164884	0.83[EUR][1000 genomes]
rs2164885	0.84[EUR][1000 genomes]
rs2268025	0.80[EUR][1000 genomes]
rs2268026	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs2268027	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2286800	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2289247	0.85[EUR][1000 genomes]
rs2289250	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2336145	0.86[EUR][1000 genomes]
rs2336146	0.81[EUR][1000 genomes]
rs2336148	0.85[EUR][1000 genomes]
rs2336149	0.83[EUR][1000 genomes]
rs2336542	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2590846	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2878726	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs33967311	0.82[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs34017441	0.89[EUR][1000 genomes]
rs34115864	0.83[EUR][1000 genomes]
rs34157897	0.85[EUR][1000 genomes]
rs34168767	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34173654	0.85[EUR][1000 genomes]
rs34215106	0.85[EUR][1000 genomes]
rs34291015	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs34537256	0.86[EUR][1000 genomes]
rs34610142	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs34610878	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs34739010	0.84[EUR][1000 genomes]
rs34754793	0.81[EUR][1000 genomes]
rs34757451	0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs34918356	0.81[EUR][1000 genomes]
rs34954168	0.81[EUR][1000 genomes]
rs35107891	0.83[EUR][1000 genomes]
rs35211965	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35249778	0.85[EUR][1000 genomes]
rs35315313	0.85[EUR][1000 genomes]
rs35409678	0.85[EUR][1000 genomes]
rs35526119	0.83[EUR][1000 genomes]
rs3733039	0.82[EUR][1000 genomes]
rs3733041	0.85[EUR][1000 genomes]
rs3733045	0.81[EUR][1000 genomes]
rs3755798	0.85[EUR][1000 genomes]
rs3755806	0.85[EUR][1000 genomes]
rs3774365	0.85[EUR][1000 genomes]
rs3774366	0.81[EUR][1000 genomes]
rs3852066	0.81[EUR][1000 genomes]
rs4130905	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4336110	0.83[EUR][1000 genomes]
rs4435633	0.83[EUR][1000 genomes]
rs4687547	0.80[EUR][1000 genomes]
rs4687548	0.85[EUR][1000 genomes]
rs4687549	0.89[EUR][1000 genomes]
rs4687633	0.85[EUR][1000 genomes]
rs4687636	0.86[EUR][1000 genomes]
rs4687637	0.81[EUR][1000 genomes]
rs4687638	0.86[EUR][1000 genomes]
rs4687639	0.84[EUR][1000 genomes]
rs4687644	0.83[EUR][1000 genomes]
rs62253700	0.85[EUR][1000 genomes]
rs62253703	0.85[EUR][1000 genomes]
rs62253733	0.86[EUR][1000 genomes]
rs62255362	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62255364	0.83[EUR][1000 genomes]
rs62255371	0.87[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62255396	0.82[EUR][1000 genomes]
rs6445529	0.81[EUR][1000 genomes]
rs6445531	0.85[EUR][1000 genomes]
rs6445534	0.85[EUR][1000 genomes]
rs6445535	0.81[EUR][1000 genomes]
rs6617	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs67539070	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs6762457	0.81[EUR][1000 genomes]
rs6762813	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6768697	0.84[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs6770463	0.85[EUR][1000 genomes]
rs6790330	0.82[EUR][1000 genomes]
rs68021750	0.85[EUR][1000 genomes]
rs6803012	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6804145	0.83[EUR][1000 genomes]
rs6976	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7611731	0.83[EUR][1000 genomes]
rs7620039	0.81[EUR][1000 genomes]
rs7622694	0.81[EUR][1000 genomes]
rs7623199	0.83[EUR][1000 genomes]
rs7624716	0.83[EUR][1000 genomes]
rs7628578	0.85[EUR][1000 genomes]
rs7638162	0.80[EUR][1000 genomes]
rs7642198	0.86[EUR][1000 genomes]
rs767418	0.84[EUR][1000 genomes]
rs8906	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9917834	0.81[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11130318	NT5DC2	cis	Skin Sun Exposed Lower leg	GTEx
rs11130318	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs11130318	PBRM1	cis	Artery Tibial	GTEx
rs11130318	GLT8D1	Cis_1M	lymphoblastoid	RTeQTL
rs11130318	PBRM1	cis	Thyroid	GTEx
rs11130318	ITIH4-AS1	cis	Whole Blood	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52721000-52738600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr3:52721400-52735800	Strong transcription	Fetal Muscle Leg	muscle
3	chr3:52722600-52736600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:52727600-52735800	Strong transcription	Osteobl	bone
5	chr3:52728400-52737600	Weak transcription	Stomach Mucosa	stomach
6	chr3:52728800-52736400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:52729000-52738600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr3:52729400-52738000	Weak transcription	Small Intestine	intestine
9	chr3:52730000-52737600	Weak transcription	Fetal Heart	heart
10	chr3:52730000-52738800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr3:52730400-52738400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:52730400-52738600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:52730600-52736400	Weak transcription	Pancreas	Pancrea
14	chr3:52730600-52737400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr3:52730600-52738600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr3:52730600-52738600	Weak transcription	Esophagus	oesophagus
17	chr3:52731600-52738600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:52731800-52735200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:52731800-52737800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr3:52732000-52736200	Weak transcription	Ovary	ovary
21	chr3:52732000-52737600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr3:52732000-52737600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr3:52732000-52737600	Weak transcription	A549	lung
24	chr3:52732000-52737600	Weak transcription	Hela-S3	cervix
25	chr3:52732000-52737600	Weak transcription	K562	blood
26	chr3:52732000-52737800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:52732000-52737800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:52732000-52737800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr3:52732000-52737800	Weak transcription	Colonic Mucosa	Colon
30	chr3:52732000-52737800	Weak transcription	Spleen	Spleen
31	chr3:52732000-52737800	Weak transcription	NHEK	skin
32	chr3:52732000-52737800	Weak transcription	NHLF	lung
33	chr3:52732000-52738000	Weak transcription	H1 Cell Line	embryonic stem cell
34	chr3:52732000-52738000	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:52732000-52738400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr3:52732000-52738400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr3:52732000-52738400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:52732000-52738600	Weak transcription	Aorta	Aorta
39	chr3:52732000-52738600	Weak transcription	Gastric	stomach
40	chr3:52732000-52738600	Weak transcription	Right Ventricle	heart
41	chr3:52732200-52736400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr3:52732200-52737600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr3:52732200-52737600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:52732200-52737600	Weak transcription	HSMMtube	muscle
45	chr3:52732200-52737800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:52732200-52737800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:52732200-52737800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr3:52732200-52737800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr3:52732200-52737800	Weak transcription	Fetal Brain Male	brain
50	chr3:52732200-52738200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

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