Variant report

Variant	rs6551279
Chromosome Location	chr3:88201304-88201305
allele	A/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	EBF1	chr3:88201263-88201466	GM12878	blood:	n/a	chr3:88201446-88201457
2	POLR2A	chr3:88198168-88201305	GM18505	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:88104745..88109799-chr3:88197543..88201780,9	MCF-7	breast:
2	chr3:88197168..88201570-chr3:88204371..88207068,4	K562	blood:
3	chr3:88106502..88110909-chr3:88195834..88201659,8	MCF-7	breast:
4	chr3:88197032..88201570-chr3:88203720..88209497,8	K562	blood:
5	chr3:88198687..88200986-chr3:88201175..88203116,4	MCF-7	breast:

Variant related genes	Relation type
CGGBP1	TF binding region
C3orf38	TF binding region
ENSG00000179021	Chromatin interaction
ENSG00000163320	Chromatin interaction
ENSG00000229729	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs11128021	0.81[EUR][1000 genomes]
rs12493327	0.82[EUR][1000 genomes]
rs13063511	0.83[ASN][1000 genomes]
rs13067419	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3890707	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4241551	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4257571	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4276211	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4337654	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4374552	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4384978	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4414876	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4429658	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4432672	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4434168	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4485742	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4488864	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4501136	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4507280	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4518156	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4555548	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4580585	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4596173	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4616670	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4858931	0.81[ASN][1000 genomes]
rs4858935	0.84[EUR][1000 genomes]
rs4858936	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4858938	0.81[AMR][1000 genomes]
rs4858995	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4858998	0.83[ASN][1000 genomes]
rs4858999	0.83[ASN][1000 genomes]
rs4859001	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55744603	0.82[EUR][1000 genomes]
rs55923163	0.81[EUR][1000 genomes]
rs55936434	0.81[EUR][1000 genomes]
rs60377014	0.81[EUR][1000 genomes]
rs6419866	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6419867	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6551271	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6551272	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6551273	0.83[ASN][1000 genomes]
rs6551274	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6551275	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6551277	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6551278	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6551280	0.86[EUR][1000 genomes]
rs6551282	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6551283	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6551284	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6551285	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6551286	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6551288	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6551289	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6551291	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6767258	0.86[ASN][1000 genomes]
rs6781333	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6782507	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6785359	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6786788	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6787824	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs6791133	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6792208	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6793783	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6796355	0.81[EUR][1000 genomes]
rs6804818	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73132515	0.81[EUR][1000 genomes]
rs7427704	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7429120	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7430158	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7432838	0.86[EUR][1000 genomes]
rs7433285	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7617691	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7618080	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7620830	0.81[EUR][1000 genomes]
rs7626777	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7628689	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7630028	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7630240	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7632123	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7635996	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7637431	0.80[EUR][1000 genomes]
rs7639420	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7641173	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7643923	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7650707	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7651641	0.86[ASN][1000 genomes]
rs7651999	0.81[ASN][1000 genomes]
rs7653652	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9310072	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9310074	0.81[ASN][1000 genomes]
rs9310077	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9813894	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9814057	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9815738	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9836364	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9841834	0.81[AMR][1000 genomes]
rs9849248	0.81[AMR][1000 genomes]
rs9854138	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9861398	0.83[ASN][1000 genomes]
rs9865335	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9865578	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9865703	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9865710	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9866843	0.81[AMR][1000 genomes]
rs9881255	0.81[AMR][1000 genomes];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	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
rs6551279	C3orf38	Cis_1M	lymphoblastoid	RTeQTL
rs6551279	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	chr3:88198000-88201400	Active TSS	Hela-S3	cervix
3	chr3:88198000-88201400	Active TSS	NHDF-Ad	bronchial
4	chr3:88199600-88203400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:88199600-88203800	Weak transcription	Spleen	Spleen
6	chr3:88199800-88202400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:88199800-88203200	Weak transcription	Lung	lung
8	chr3:88199800-88204000	Weak transcription	Gastric	stomach
9	chr3:88199800-88216800	Weak transcription	Esophagus	oesophagus
10	chr3:88200000-88201400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
11	chr3:88200000-88202400	Weak transcription	Left Ventricle	heart
12	chr3:88200000-88202400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:88200000-88202600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:88200000-88203800	Weak transcription	Placenta Amnion	Placenta Amnion
15	chr3:88200200-88201400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr3:88200200-88202400	Weak transcription	Small Intestine	intestine
17	chr3:88200200-88202600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr3:88200200-88205600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr3:88200400-88201400	Enhancers	Liver	Liver
20	chr3:88200400-88201400	Flanking Active TSS	Dnd41	blood
21	chr3:88200400-88202000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:88200400-88202000	Weak transcription	Placenta	Placenta
23	chr3:88200400-88202600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr3:88200400-88203400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:88200600-88201400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:88200600-88201400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr3:88200800-88201400	Enhancers	Adipose Nuclei	Adipose
28	chr3:88200800-88201400	Enhancers	Brain Hippocampus Middle	brain
29	chr3:88200800-88201400	Enhancers	Colon Smooth Muscle	Colon
30	chr3:88200800-88201400	Enhancers	Fetal Lung	lung
31	chr3:88200800-88201400	Enhancers	Thymus	Thymus
32	chr3:88200800-88201400	Enhancers	HepG2	liver
33	chr3:88200800-88201800	Enhancers	Fetal Thymus	thymus
34	chr3:88200800-88202400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:88200800-88202400	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr3:88200800-88202400	Enhancers	Primary B cells from peripheral blood	blood
37	chr3:88200800-88202600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr3:88200800-88202600	Enhancers	Primary T cells fromperipheralblood	blood
39	chr3:88200800-88202600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr3:88200800-88202800	Weak transcription	Fetal Stomach	stomach
41	chr3:88200800-88203400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:88200800-88204000	Weak transcription	Fetal Intestine Small	intestine
43	chr3:88200800-88204000	Weak transcription	Ovary	ovary
44	chr3:88200800-88204800	Weak transcription	Right Ventricle	heart
45	chr3:88200800-88205200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr3:88200800-88209400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr3:88200800-88214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr3:88200800-88218000	Weak transcription	Pancreas	Pancrea
49	chr3:88200800-88221600	Weak transcription	Psoas Muscle	Psoas
50	chr3:88200800-88224400	Weak transcription	Aorta	Aorta

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