Variant report

Variant	rs6551280
Chromosome Location	chr3:88201739-88201740
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:88104745..88109799-chr3:88197543..88201780,9	MCF-7	breast:
2	chr3:88198687..88200986-chr3:88201175..88203116,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163320	Chromatin interaction
ENSG00000229729	Chromatin interaction
ENSG00000179021	Chromatin interaction

Extended variants
information (count: 154 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:153)

rs_ID	r²[population]
rs11128021	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12493327	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631689	0.90[EUR][1000 genomes]
rs12714702	0.85[EUR][1000 genomes]
rs13060704	0.90[EUR][1000 genomes]
rs13063511	0.92[EUR][1000 genomes]
rs13067183	0.88[EUR][1000 genomes]
rs13067419	0.93[EUR][1000 genomes]
rs13317261	0.90[EUR][1000 genomes]
rs28672845	0.82[EUR][1000 genomes]
rs28694532	0.85[EUR][1000 genomes]
rs3890707	0.99[EUR][1000 genomes]
rs4241551	0.93[EUR][1000 genomes]
rs4257571	0.95[EUR][1000 genomes]
rs4276211	0.91[EUR][1000 genomes]
rs4276212	0.91[EUR][1000 genomes]
rs4337654	0.95[EUR][1000 genomes]
rs4374552	0.95[EUR][1000 genomes]
rs4384978	0.95[EUR][1000 genomes]
rs4402954	0.85[EUR][1000 genomes]
rs4407422	0.88[EUR][1000 genomes]
rs4414876	0.95[EUR][1000 genomes]
rs4429658	0.93[EUR][1000 genomes]
rs4432672	0.95[EUR][1000 genomes]
rs4434168	0.93[EUR][1000 genomes]
rs4485742	0.95[EUR][1000 genomes]
rs4488864	0.95[EUR][1000 genomes]
rs4501136	0.95[EUR][1000 genomes]
rs4507280	0.95[EUR][1000 genomes]
rs4518156	0.95[EUR][1000 genomes]
rs4555548	0.95[EUR][1000 genomes]
rs4580585	0.95[EUR][1000 genomes]
rs4596173	0.95[EUR][1000 genomes]
rs4616670	0.92[EUR][1000 genomes]
rs4858931	0.90[EUR][1000 genomes]
rs4858935	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4858936	0.97[EUR][1000 genomes]
rs4858937	0.90[EUR][1000 genomes]
rs4858938	0.88[EUR][1000 genomes]
rs4858995	0.93[EUR][1000 genomes]
rs4858998	0.92[EUR][1000 genomes]
rs4858999	0.88[EUR][1000 genomes]
rs4859001	0.97[EUR][1000 genomes]
rs4859002	0.90[EUR][1000 genomes]
rs4859004	0.88[EUR][1000 genomes]
rs4859005	0.88[EUR][1000 genomes]
rs55744603	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55923163	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55936434	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60377014	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6419866	0.83[EUR][1000 genomes]
rs6419867	0.87[EUR][1000 genomes]
rs6551271	0.93[EUR][1000 genomes]
rs6551272	0.95[EUR][1000 genomes]
rs6551273	0.92[EUR][1000 genomes]
rs6551274	0.95[EUR][1000 genomes]
rs6551275	0.99[EUR][1000 genomes]
rs6551277	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6551278	0.99[EUR][1000 genomes]
rs6551279	0.86[EUR][1000 genomes]
rs6551282	0.99[EUR][1000 genomes]
rs6551283	0.96[EUR][1000 genomes]
rs6551284	0.97[EUR][1000 genomes]
rs6551285	0.97[EUR][1000 genomes]
rs6551286	0.97[EUR][1000 genomes]
rs6551288	0.97[EUR][1000 genomes]
rs6551289	0.97[EUR][1000 genomes]
rs6551291	0.95[EUR][1000 genomes]
rs6551292	0.88[EUR][1000 genomes]
rs6551293	0.88[EUR][1000 genomes]
rs6551294	0.88[EUR][1000 genomes]
rs6551296	0.85[EUR][1000 genomes]
rs6551297	0.85[EUR][1000 genomes]
rs6551298	0.85[EUR][1000 genomes]
rs6762453	0.87[EUR][1000 genomes]
rs6767258	0.92[EUR][1000 genomes]
rs6771031	0.88[EUR][1000 genomes]
rs6778708	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6781333	0.99[EUR][1000 genomes]
rs6782507	0.95[EUR][1000 genomes]
rs6785359	0.97[EUR][1000 genomes]
rs6785560	0.85[EUR][1000 genomes]
rs6786788	0.93[EUR][1000 genomes]
rs6787824	0.91[EUR][1000 genomes]
rs6791133	0.99[EUR][1000 genomes]
rs6792208	0.93[EUR][1000 genomes]
rs6793783	0.93[EUR][1000 genomes]
rs6796355	0.91[EUR][1000 genomes]
rs6801046	0.88[EUR][1000 genomes]
rs6804818	0.93[EUR][1000 genomes]
rs6805804	0.81[EUR][1000 genomes]
rs6805957	0.88[EUR][1000 genomes]
rs73132515	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7427047	0.88[EUR][1000 genomes]
rs7427296	0.86[EUR][1000 genomes]
rs7427335	0.88[EUR][1000 genomes]
rs7427704	0.92[EUR][1000 genomes]
rs7428357	0.88[EUR][1000 genomes]
rs7429120	0.99[EUR][1000 genomes]
rs7430158	0.99[EUR][1000 genomes]
rs7431074	0.87[EUR][1000 genomes]
rs7432509	0.88[EUR][1000 genomes]
rs7432838	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433285	0.97[EUR][1000 genomes]
rs7615585	0.88[EUR][1000 genomes]
rs7617691	0.99[EUR][1000 genomes]
rs7618080	0.95[EUR][1000 genomes]
rs7620830	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7626777	0.93[EUR][1000 genomes]
rs7628689	0.96[EUR][1000 genomes]
rs7630028	0.93[EUR][1000 genomes]
rs7630240	0.94[EUR][1000 genomes]
rs7632123	0.97[EUR][1000 genomes]
rs7635996	0.93[EUR][1000 genomes]
rs7639420	0.95[EUR][1000 genomes]
rs7641173	0.95[EUR][1000 genomes]
rs7643923	0.90[EUR][1000 genomes]
rs7650707	0.95[EUR][1000 genomes]
rs7651641	0.92[EUR][1000 genomes]
rs7651999	0.88[EUR][1000 genomes]
rs7652528	0.90[EUR][1000 genomes]
rs7653652	0.99[EUR][1000 genomes]
rs9310072	0.93[EUR][1000 genomes]
rs9310074	0.90[EUR][1000 genomes]
rs9310077	0.99[EUR][1000 genomes]
rs9809661	0.88[EUR][1000 genomes]
rs9813894	0.97[EUR][1000 genomes]
rs9814057	0.97[EUR][1000 genomes]
rs9815738	0.82[EUR][1000 genomes]
rs9831230	0.88[EUR][1000 genomes]
rs9832011	0.87[EUR][1000 genomes]
rs9834468	0.91[EUR][1000 genomes]
rs9836364	0.85[EUR][1000 genomes]
rs9839322	0.83[EUR][1000 genomes]
rs9841834	0.88[EUR][1000 genomes]
rs9843550	0.88[EUR][1000 genomes]
rs9847355	0.88[EUR][1000 genomes]
rs9848258	0.88[EUR][1000 genomes]
rs9849248	0.88[EUR][1000 genomes]
rs9849353	0.88[EUR][1000 genomes]
rs9854138	0.99[EUR][1000 genomes]
rs9856990	0.85[EUR][1000 genomes]
rs9861398	0.92[EUR][1000 genomes]
rs9865335	0.97[EUR][1000 genomes]
rs9865578	0.99[EUR][1000 genomes]
rs9865703	0.99[EUR][1000 genomes]
rs9865710	0.99[EUR][1000 genomes]
rs9866843	0.88[EUR][1000 genomes]
rs9868310	0.86[EUR][1000 genomes]
rs9868977	0.88[EUR][1000 genomes]
rs9873182	0.85[EUR][1000 genomes]
rs9876807	0.88[EUR][1000 genomes]
rs9881255	0.93[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
rs6551280	C3orf38	Cis_1M	lymphoblastoid	RTeQTL
rs6551280	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88196200-88202000	Active TSS	GM12878-XiMat	blood
2	chr3:88199600-88203400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr3:88199600-88203800	Weak transcription	Spleen	Spleen
4	chr3:88199800-88202400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:88199800-88203200	Weak transcription	Lung	lung
6	chr3:88199800-88204000	Weak transcription	Gastric	stomach
7	chr3:88199800-88216800	Weak transcription	Esophagus	oesophagus
8	chr3:88200000-88202400	Weak transcription	Left Ventricle	heart
9	chr3:88200000-88202400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:88200000-88202600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:88200000-88203800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr3:88200200-88202400	Weak transcription	Small Intestine	intestine
13	chr3:88200200-88202600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:88200200-88205600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr3:88200400-88202000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:88200400-88202000	Weak transcription	Placenta	Placenta
17	chr3:88200400-88202600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
18	chr3:88200400-88203400	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr3:88200800-88201800	Enhancers	Fetal Thymus	thymus
20	chr3:88200800-88202400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr3:88200800-88202400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr3:88200800-88202400	Enhancers	Primary B cells from peripheral blood	blood
23	chr3:88200800-88202600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr3:88200800-88202600	Enhancers	Primary T cells fromperipheralblood	blood
25	chr3:88200800-88202600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr3:88200800-88202800	Weak transcription	Fetal Stomach	stomach
27	chr3:88200800-88203400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:88200800-88204000	Weak transcription	Fetal Intestine Small	intestine
29	chr3:88200800-88204000	Weak transcription	Ovary	ovary
30	chr3:88200800-88204800	Weak transcription	Right Ventricle	heart
31	chr3:88200800-88205200	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr3:88200800-88209400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr3:88200800-88214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:88200800-88218000	Weak transcription	Pancreas	Pancrea
35	chr3:88200800-88221600	Weak transcription	Psoas Muscle	Psoas
36	chr3:88200800-88224400	Weak transcription	Aorta	Aorta
37	chr3:88201000-88202200	Enhancers	Primary B cells from cord blood	blood
38	chr3:88201000-88202400	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr3:88201000-88202400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr3:88201000-88203000	Weak transcription	Fetal Kidney	kidney
41	chr3:88201000-88203600	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr3:88201000-88203600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:88201000-88205200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr3:88201200-88201800	Enhancers	Fetal Brain Female	brain
45	chr3:88201200-88201800	Enhancers	Monocytes-CD14+_RO01746	blood
46	chr3:88201200-88202000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr3:88201200-88202000	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:88201200-88202000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
49	chr3:88201200-88202000	Enhancers	Brain Germinal Matrix	brain
50	chr3:88201200-88202200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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