Variant report

Variant	rs4273396
Chromosome Location	chr3:88119743-88119744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:88118437..88120288-chr3:88196139..88198741,2	MCF-7	breast:
2	chr3:88117841..88121656-chr3:88124313..88127922,3	MCF-7	breast:
3	chr3:88114310..88116574-chr3:88119594..88122386,2	MCF-7	breast:
4	chr21:38341134..38341883-chr3:88119321..88120209,2	MCF-7	breast:

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs1006895	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1040319	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1051413	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1051436	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1063597	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1063603	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10865625	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12495016	0.86[EUR][1000 genomes]
rs12632529	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13060730	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13063511	0.80[ASN][1000 genomes]
rs13067419	0.83[ASN][1000 genomes]
rs13076170	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13098157	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1991659	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2049817	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2116149	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3732776	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4276211	0.83[ASN][1000 genomes]
rs4276212	0.82[ASN][1000 genomes]
rs4368523	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4378991	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4384978	0.80[ASN][1000 genomes]
rs4416403	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4429658	0.83[ASN][1000 genomes]
rs4432672	0.80[ASN][1000 genomes]
rs4434168	0.83[ASN][1000 genomes]
rs4438681	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4485742	0.80[ASN][1000 genomes]
rs4488864	0.80[ASN][1000 genomes]
rs4502603	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4555548	0.80[ASN][1000 genomes]
rs4580585	0.80[ASN][1000 genomes]
rs4588391	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4611846	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4616670	0.85[ASN][1000 genomes]
rs4638995	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858931	0.83[ASN][1000 genomes]
rs4858981	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858982	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858983	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858985	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858992	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858994	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4858995	0.85[ASN][1000 genomes]
rs4858998	0.80[ASN][1000 genomes]
rs4858999	0.80[ASN][1000 genomes]
rs6551268	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6551271	0.83[ASN][1000 genomes]
rs6551272	0.80[ASN][1000 genomes]
rs6551273	0.80[ASN][1000 genomes]
rs6777019	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6786788	0.83[ASN][1000 genomes]
rs6787824	0.83[ASN][1000 genomes]
rs6790426	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6790629	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6792208	0.85[ASN][1000 genomes]
rs6793783	0.85[ASN][1000 genomes]
rs6796355	0.80[ASN][1000 genomes]
rs6799233	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6804818	0.83[ASN][1000 genomes]
rs7618080	0.80[ASN][1000 genomes]
rs7618472	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7626777	0.83[ASN][1000 genomes]
rs7630028	0.83[ASN][1000 genomes]
rs7633121	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7635996	0.83[ASN][1000 genomes]
rs7639420	0.80[ASN][1000 genomes]
rs7643923	0.83[ASN][1000 genomes]
rs7648096	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7650707	0.83[ASN][1000 genomes]
rs7651999	0.83[ASN][1000 genomes]
rs9310066	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9310067	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9310068	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9310072	0.85[ASN][1000 genomes]
rs9310074	0.83[ASN][1000 genomes]
rs959048	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs959049	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs959050	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9821517	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9829873	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9832011	0.84[ASN][1000 genomes]
rs9834501	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9835178	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9835771	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9840953	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9841189	0.84[AFR][1000 genomes]
rs9845776	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9846115	0.88[ASN][1000 genomes]
rs9847019	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9850892	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9851328	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9861398	0.80[ASN][1000 genomes]
rs9864220	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9865990	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9866349	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9870952	0.82[AFR][1000 genomes]
rs9872602	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9879044	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9881255	0.85[ASN][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
rs4273396	C3orf38	Cis_1M	lymphoblastoid	RTeQTL
rs4273396	CGGBP1///LOC728397	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:88109400-88124400	Weak transcription	Pancreas	Pancrea
2	chr3:88110000-88120400	Weak transcription	Fetal Stomach	stomach
3	chr3:88110000-88120400	Weak transcription	Fetal Thymus	thymus
4	chr3:88110000-88121000	Weak transcription	Primary B cells from peripheral blood	blood
5	chr3:88110200-88124200	Weak transcription	Fetal Kidney	kidney
6	chr3:88110400-88120200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr3:88111400-88121600	Weak transcription	Fetal Brain Male	brain
8	chr3:88111400-88124200	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr3:88111400-88133600	Weak transcription	Brain Angular Gyrus	brain
10	chr3:88111400-88136200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr3:88111400-88136200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr3:88111600-88119800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr3:88111600-88121200	Weak transcription	NHLF	lung
14	chr3:88111600-88123200	Weak transcription	Liver	Liver
15	chr3:88111600-88124000	Weak transcription	Right Atrium	heart
16	chr3:88111600-88124000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr3:88111600-88124000	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr3:88111600-88124200	Weak transcription	Fetal Lung	lung
19	chr3:88111600-88135200	Weak transcription	HSMM	muscle
20	chr3:88111600-88135400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr3:88111600-88135600	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr3:88111800-88123600	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr3:88111800-88135400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
24	chr3:88112200-88136600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr3:88112200-88154200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr3:88112400-88121200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr3:88112400-88124400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr3:88112400-88143600	Weak transcription	HUVEC	blood vessel
29	chr3:88113200-88146200	Weak transcription	HMEC	breast
30	chr3:88113600-88121400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr3:88113800-88123000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:88113800-88134800	Weak transcription	Dnd41	blood
33	chr3:88114000-88122400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr3:88115200-88133400	Weak transcription	Left Ventricle	heart
35	chr3:88115600-88119800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:88115600-88120400	Weak transcription	Fetal Intestine Small	intestine
37	chr3:88115600-88124000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
38	chr3:88116800-88124200	Weak transcription	Brain Hippocampus Middle	brain
39	chr3:88116800-88139800	Weak transcription	Thymus	Thymus
40	chr3:88117000-88121600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr3:88117000-88124400	Weak transcription	Right Ventricle	heart
42	chr3:88117000-88133800	Weak transcription	Aorta	Aorta
43	chr3:88117000-88135800	Weak transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:88117400-88124600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr3:88117600-88121200	Weak transcription	Primary B cells from cord blood	blood
46	chr3:88117600-88122400	Weak transcription	Primary T cells from cord blood	blood
47	chr3:88117600-88123800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr3:88118000-88121600	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:88118000-88124200	Weak transcription	Fetal Heart	heart
50	chr3:88118000-88128800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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