Variant report

Variant	rs4407422
Chromosome Location	chr3:88153013-88153014
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:88142483..88144526-chr3:88152131..88154369,2	MCF-7	breast:

Extended variants
information (count: 136 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs11128021	0.94[EUR][1000 genomes]
rs12493327	0.92[EUR][1000 genomes]
rs12631689	0.81[EUR][1000 genomes]
rs13060704	0.81[EUR][1000 genomes]
rs13063511	0.89[EUR][1000 genomes]
rs13067419	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13317261	0.81[EUR][1000 genomes]
rs3890707	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4241551	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4257571	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4276211	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4276212	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4337654	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4374552	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4378991	0.85[AFR][1000 genomes]
rs4384978	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4402954	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4414876	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4416403	0.86[AFR][1000 genomes]
rs4429658	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4432672	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4434168	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4438681	0.86[AFR][1000 genomes]
rs4485742	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4488864	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4501136	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4507280	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4518156	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4555548	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4568164	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs4580585	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4596173	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4616670	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4858931	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4858935	0.87[EUR][1000 genomes]
rs4858936	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4858937	0.81[EUR][1000 genomes]
rs4858992	0.81[AFR][1000 genomes]
rs4858994	0.83[AFR][1000 genomes]
rs4858995	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4858997	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4858998	0.89[EUR][1000 genomes]
rs4858999	0.86[EUR][1000 genomes]
rs4859001	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4859002	0.81[EUR][1000 genomes]
rs5024149	0.82[AFR][1000 genomes]
rs55744603	0.92[EUR][1000 genomes]
rs55923163	0.94[EUR][1000 genomes]
rs55936434	0.94[EUR][1000 genomes]
rs60377014	0.90[EUR][1000 genomes]
rs6419866	0.83[AFR][1000 genomes]
rs6551268	0.86[AFR][1000 genomes]
rs6551271	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6551272	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6551273	0.89[EUR][1000 genomes]
rs6551274	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6551275	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6551277	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6551278	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6551280	0.88[EUR][1000 genomes]
rs6551282	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6551283	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6551284	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6551285	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6551286	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6551288	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6551289	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6551291	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6767258	0.89[EUR][1000 genomes]
rs6781333	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6782507	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6785359	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6786788	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6787824	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6790426	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6790629	0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs6791133	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6792208	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6793783	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6796355	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6799233	0.86[AFR][1000 genomes]
rs6804818	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6805804	0.82[AMR][1000 genomes]
rs73132515	0.94[EUR][1000 genomes]
rs7427704	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7429120	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7430158	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7431074	0.80[AMR][1000 genomes]
rs7432838	0.88[EUR][1000 genomes]
rs7433285	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7617691	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7618080	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7618472	0.86[AFR][1000 genomes]
rs7620830	0.94[EUR][1000 genomes]
rs7626777	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7628689	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7630028	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7630240	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7632123	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7633121	0.81[AFR][1000 genomes]
rs7635996	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7639420	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7641173	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7643923	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7648096	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7650707	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7651641	0.89[EUR][1000 genomes]
rs7651999	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7652528	0.81[EUR][1000 genomes]
rs7653652	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9310067	0.81[AFR][1000 genomes]
rs9310068	0.83[AFR][1000 genomes]
rs9310072	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9310074	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9310077	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9813894	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9814057	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9815738	0.82[AFR][1000 genomes]
rs9829873	0.86[AFR][1000 genomes]
rs9832011	0.89[EUR][1000 genomes]
rs9834468	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9835771	0.86[AFR][1000 genomes]
rs9836364	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs9839322	0.82[EUR][1000 genomes]
rs9845776	0.86[AFR][1000 genomes]
rs9847019	0.86[AFR][1000 genomes]
rs9854138	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9861398	0.89[EUR][1000 genomes]
rs9865335	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9865578	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9865703	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9865710	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9872602	0.86[AFR][1000 genomes]
rs9881255	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv877146	chr3:87983962-88159835	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	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
rs4407422	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL
rs4407422	C3orf38	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88112200-88154200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr3:88125200-88163600	Weak transcription	NHDF-Ad	bronchial
3	chr3:88128800-88198200	Weak transcription	Esophagus	oesophagus
4	chr3:88129600-88180200	Weak transcription	NHEK	skin
5	chr3:88130600-88155000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:88133800-88155400	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr3:88134000-88176400	Weak transcription	Ovary	ovary
8	chr3:88134200-88154400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr3:88134200-88159400	Weak transcription	Fetal Heart	heart
10	chr3:88134800-88188200	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:88135600-88196800	Weak transcription	Hela-S3	cervix
12	chr3:88137200-88155000	Weak transcription	Left Ventricle	heart
13	chr3:88137200-88162600	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:88137400-88155400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr3:88137400-88163800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:88137400-88188200	Weak transcription	Fetal Kidney	kidney
17	chr3:88138200-88180800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:88139200-88163800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr3:88140200-88163800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:88140400-88154400	Weak transcription	Adipose Nuclei	Adipose
21	chr3:88140400-88163800	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr3:88140400-88167000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr3:88140600-88163200	Weak transcription	Fetal Intestine Large	intestine
24	chr3:88140600-88163600	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr3:88140800-88162600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr3:88140800-88162600	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr3:88140800-88162600	Weak transcription	HSMM	muscle
28	chr3:88140800-88163200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:88140800-88163400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:88140800-88176000	Weak transcription	K562	blood
31	chr3:88141000-88163600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr3:88141000-88163800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:88141000-88165200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:88141000-88197800	Weak transcription	Thymus	Thymus
35	chr3:88141200-88163400	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr3:88141200-88163600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:88141200-88167200	Weak transcription	Liver	Liver
38	chr3:88141200-88182200	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr3:88141400-88162400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr3:88142800-88154600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr3:88145200-88191000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:88145200-88198200	Weak transcription	Aorta	Aorta
43	chr3:88146400-88162600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr3:88146400-88167400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr3:88146600-88154600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr3:88146600-88157400	Weak transcription	Primary T cells from cord blood	blood
47	chr3:88146600-88162600	Weak transcription	Fetal Thymus	thymus
48	chr3:88146600-88162800	Weak transcription	Fetal Lung	lung
49	chr3:88146600-88163000	Weak transcription	Dnd41	blood
50	chr3:88146600-88163200	Weak transcription	Monocytes-CD14+_RO01746	blood

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