Variant report

Variant	rs60377014
Chromosome Location	chr3:88187052-88187053
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	REST	chr3:88187042-88187346	H1-neurons	neurons:	n/a	n/a
2	FOS	chr3:88186986-88187374	MCF10A-Er-Src	breast:	n/a	chr3:88187194-88187202 chr3:88187192-88187204 chr3:88187195-88187202
3	FOS	chr3:88187004-88187369	MCF10A-Er-Src	breast:	n/a	chr3:88187194-88187202 chr3:88187192-88187204 chr3:88187195-88187202
4	CTCF	chr3:88187000-88187150	HPAF	blood vessel:	n/a	n/a
5	FOS	chr3:88187027-88187346	MCF10A-Er-Src	breast:	n/a	chr3:88187194-88187202 chr3:88187192-88187204 chr3:88187195-88187202
6	CEBPB	chr3:88187002-88187364	IMR90	lung:	n/a	n/a
7	CEBPB	chr3:88187025-88187319	Hela-S3	cervix:	n/a	n/a
8	STAT3	chr3:88187036-88187340	MCF10A-Er-Src	breast:	n/a	n/a
9	FOS	chr3:88187010-88187408	MCF10A-Er-Src	breast:	n/a	chr3:88187194-88187202 chr3:88187192-88187204 chr3:88187195-88187202

No.	Distal block	Cell Line	Cell type
1	chr3:88181347..88191666-chr3:88192147..88201015,17	MCF-7	breast:
2	chr3:88184541..88187241-chr3:88188929..88190940,2	K562	blood:
3	chr3:88184501..88187233-chr3:88191111..88195039,3	K562	blood:
4	chr3:88186405..88188114-chr3:88197534..88199508,2	MCF-7	breast:

Variant related genes	Relation type
ZNF654	TF binding region
ENSG00000179021	Chromatin interaction
ENSG00000163320	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:147)

rs_ID	r²[population]
rs11128021	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12493327	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631689	0.84[EUR][1000 genomes]
rs13060704	0.84[EUR][1000 genomes]
rs13063511	0.94[EUR][1000 genomes]
rs13067183	0.83[EUR][1000 genomes]
rs13067419	0.95[EUR][1000 genomes]
rs13317261	0.84[EUR][1000 genomes]
rs28694532	0.80[EUR][1000 genomes]
rs3890707	0.93[EUR][1000 genomes]
rs4241551	0.95[EUR][1000 genomes]
rs4257571	0.97[EUR][1000 genomes]
rs4276211	0.93[EUR][1000 genomes]
rs4276212	0.93[EUR][1000 genomes]
rs4337654	0.97[EUR][1000 genomes]
rs4374552	0.97[EUR][1000 genomes]
rs4384978	0.97[EUR][1000 genomes]
rs4402954	0.87[EUR][1000 genomes]
rs4407422	0.90[EUR][1000 genomes]
rs4414876	0.97[EUR][1000 genomes]
rs4429658	0.95[EUR][1000 genomes]
rs4432672	0.97[EUR][1000 genomes]
rs4434168	0.95[EUR][1000 genomes]
rs4485742	0.97[EUR][1000 genomes]
rs4488864	0.97[EUR][1000 genomes]
rs4501136	0.97[EUR][1000 genomes]
rs4507280	0.97[EUR][1000 genomes]
rs4518156	0.97[EUR][1000 genomes]
rs4555548	0.97[EUR][1000 genomes]
rs4580585	0.97[EUR][1000 genomes]
rs4596173	0.97[EUR][1000 genomes]
rs4616670	0.96[EUR][1000 genomes]
rs4858931	0.92[EUR][1000 genomes]
rs4858935	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858936	0.92[EUR][1000 genomes]
rs4858937	0.84[EUR][1000 genomes]
rs4858938	0.83[EUR][1000 genomes]
rs4858995	0.95[EUR][1000 genomes]
rs4858997	0.82[EUR][1000 genomes]
rs4858998	0.94[EUR][1000 genomes]
rs4858999	0.90[EUR][1000 genomes]
rs4859001	0.92[EUR][1000 genomes]
rs4859002	0.84[EUR][1000 genomes]
rs4859004	0.83[EUR][1000 genomes]
rs4859005	0.83[EUR][1000 genomes]
rs55744603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55923163	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55936434	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6419867	0.82[EUR][1000 genomes]
rs6551271	0.94[EUR][1000 genomes]
rs6551272	0.97[EUR][1000 genomes]
rs6551273	0.94[EUR][1000 genomes]
rs6551274	0.97[EUR][1000 genomes]
rs6551275	0.93[EUR][1000 genomes]
rs6551277	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6551278	0.93[EUR][1000 genomes]
rs6551279	0.81[EUR][1000 genomes]
rs6551280	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6551282	0.93[EUR][1000 genomes]
rs6551283	0.91[EUR][1000 genomes]
rs6551284	0.92[EUR][1000 genomes]
rs6551285	0.92[EUR][1000 genomes]
rs6551286	0.92[EUR][1000 genomes]
rs6551288	0.92[EUR][1000 genomes]
rs6551289	0.92[EUR][1000 genomes]
rs6551291	0.90[EUR][1000 genomes]
rs6551292	0.83[EUR][1000 genomes]
rs6551293	0.83[EUR][1000 genomes]
rs6551294	0.83[EUR][1000 genomes]
rs6551296	0.80[EUR][1000 genomes]
rs6551298	0.80[EUR][1000 genomes]
rs6762453	0.82[EUR][1000 genomes]
rs6767258	0.94[EUR][1000 genomes]
rs6771031	0.83[EUR][1000 genomes]
rs6778708	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6781333	0.93[EUR][1000 genomes]
rs6782507	0.97[EUR][1000 genomes]
rs6785359	0.92[EUR][1000 genomes]
rs6785560	0.80[EUR][1000 genomes]
rs6786788	0.95[EUR][1000 genomes]
rs6787824	0.92[EUR][1000 genomes]
rs6791133	0.93[EUR][1000 genomes]
rs6792208	0.95[EUR][1000 genomes]
rs6793783	0.95[EUR][1000 genomes]
rs6796355	0.93[EUR][1000 genomes]
rs6801046	0.83[EUR][1000 genomes]
rs6804818	0.95[EUR][1000 genomes]
rs6805957	0.83[EUR][1000 genomes]
rs73132515	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7427047	0.83[EUR][1000 genomes]
rs7427296	0.81[EUR][1000 genomes]
rs7427335	0.83[EUR][1000 genomes]
rs7427704	0.86[EUR][1000 genomes]
rs7428357	0.83[EUR][1000 genomes]
rs7429120	0.93[EUR][1000 genomes]
rs7430158	0.93[EUR][1000 genomes]
rs7431074	0.82[EUR][1000 genomes]
rs7432509	0.83[EUR][1000 genomes]
rs7432838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433285	0.92[EUR][1000 genomes]
rs7615585	0.83[EUR][1000 genomes]
rs7617691	0.93[EUR][1000 genomes]
rs7618080	0.97[EUR][1000 genomes]
rs7620830	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7626777	0.95[EUR][1000 genomes]
rs7628689	0.91[EUR][1000 genomes]
rs7630028	0.95[EUR][1000 genomes]
rs7630240	0.96[EUR][1000 genomes]
rs7632123	0.92[EUR][1000 genomes]
rs7635996	0.95[EUR][1000 genomes]
rs7639420	0.97[EUR][1000 genomes]
rs7641173	0.90[EUR][1000 genomes]
rs7643923	0.92[EUR][1000 genomes]
rs7650707	0.97[EUR][1000 genomes]
rs7651641	0.94[EUR][1000 genomes]
rs7651999	0.90[EUR][1000 genomes]
rs7652528	0.84[EUR][1000 genomes]
rs7653652	0.93[EUR][1000 genomes]
rs9310072	0.95[EUR][1000 genomes]
rs9310074	0.92[EUR][1000 genomes]
rs9310077	0.93[EUR][1000 genomes]
rs9809661	0.83[EUR][1000 genomes]
rs9813894	0.95[EUR][1000 genomes]
rs9814057	0.92[EUR][1000 genomes]
rs9831230	0.83[EUR][1000 genomes]
rs9832011	0.88[EUR][1000 genomes]
rs9834468	0.93[EUR][1000 genomes]
rs9836364	0.87[EUR][1000 genomes]
rs9839322	0.85[EUR][1000 genomes]
rs9841834	0.83[EUR][1000 genomes]
rs9843550	0.83[EUR][1000 genomes]
rs9847355	0.83[EUR][1000 genomes]
rs9848258	0.83[EUR][1000 genomes]
rs9849248	0.83[EUR][1000 genomes]
rs9849353	0.83[EUR][1000 genomes]
rs9854138	0.93[EUR][1000 genomes]
rs9856990	0.80[EUR][1000 genomes]
rs9861398	0.94[EUR][1000 genomes]
rs9865335	0.92[EUR][1000 genomes]
rs9865578	0.93[EUR][1000 genomes]
rs9865703	0.93[EUR][1000 genomes]
rs9865710	0.93[EUR][1000 genomes]
rs9866843	0.83[EUR][1000 genomes]
rs9868310	0.81[EUR][1000 genomes]
rs9868977	0.83[EUR][1000 genomes]
rs9876807	0.83[EUR][1000 genomes]
rs9881255	0.95[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	nsv916330	chr3:88083580-88884125	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs60377014	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL
rs60377014	C3orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88128800-88198200	Weak transcription	Esophagus	oesophagus
2	chr3:88134800-88188200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr3:88135600-88196800	Weak transcription	Hela-S3	cervix
4	chr3:88137400-88188200	Weak transcription	Fetal Kidney	kidney
5	chr3:88141000-88197800	Weak transcription	Thymus	Thymus
6	chr3:88145200-88191000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:88145200-88198200	Weak transcription	Aorta	Aorta
8	chr3:88148000-88196400	Weak transcription	Fetal Intestine Small	intestine
9	chr3:88152000-88197000	Weak transcription	Lung	lung
10	chr3:88155400-88188000	Weak transcription	Psoas Muscle	Psoas
11	chr3:88155400-88188200	Weak transcription	Right Ventricle	heart
12	chr3:88155800-88189200	Weak transcription	Colonic Mucosa	Colon
13	chr3:88156000-88189000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:88159600-88197800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:88161000-88197800	Weak transcription	Fetal Stomach	stomach
16	chr3:88162200-88188000	Weak transcription	NHLF	lung
17	chr3:88162800-88187800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:88162800-88191600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr3:88162800-88197200	Weak transcription	Brain Cingulate Gyrus	brain
20	chr3:88162800-88198000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr3:88163600-88197800	Weak transcription	Gastric	stomach
22	chr3:88163800-88188400	Weak transcription	Fetal Brain Female	brain
23	chr3:88164200-88188200	Weak transcription	Left Ventricle	heart
24	chr3:88165600-88188000	Weak transcription	Fetal Muscle Trunk	muscle
25	chr3:88166000-88188400	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr3:88166000-88190800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr3:88166200-88188200	Weak transcription	Fetal Brain Male	brain
28	chr3:88167600-88188400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
29	chr3:88167600-88197800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr3:88168000-88197800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:88171000-88198000	Weak transcription	Small Intestine	intestine
32	chr3:88171400-88198000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr3:88175000-88192000	Strong transcription	Primary monocytes fromperipheralblood	blood
34	chr3:88175800-88197800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr3:88176400-88191800	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr3:88176800-88189200	Weak transcription	K562	blood
37	chr3:88177000-88188200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:88177400-88197800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr3:88178000-88192000	Strong transcription	Dnd41	blood
40	chr3:88178200-88192000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:88178800-88188200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr3:88178800-88188200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:88179400-88190000	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr3:88179600-88187200	Strong transcription	Primary hematopoietic stem cells	blood
45	chr3:88179600-88190400	Strong transcription	Liver	Liver
46	chr3:88179600-88197800	Weak transcription	Spleen	Spleen
47	chr3:88179800-88189400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr3:88179800-88191600	Strong transcription	Fetal Thymus	thymus
49	chr3:88179800-88197800	Weak transcription	Pancreas	Pancrea
50	chr3:88180000-88192000	Strong transcription	Adipose Nuclei	Adipose

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